I would like to question two statements you make because they paint an oversimplified picture, which unfortunately is alluring to mathematicians who do not want to think about foundations (and they should not be blamed for it anymore than I should be blamed for not wanting to think about PDEs).
"Most mathematicians accept as given the ZFC (or at least ZF) axioms for sets." This is what mathematicians say, but most cannot even tell you what ZFC is. Mathematicians work at a more intuitive and informal manner. High party officials once declared that ZFC was being used by everyone, so it has become the party line. But if you read a random text of mathematics, it will be equally easy to interpret it in other kinds of foundations, such as type theory, bounded Zermelo set theory, etc. They do not use the language of ZFC. The language of ZFC is completely unusable for the working mathematician, as it only has a single relation symbol $\in$. As soon as you allow in abbreviations, your exposition becomes expressible more naturally in other formal systems that actually handle abbreviations formally. Informal mathematics is informal, and thankfully, it does not require any foundation to function, just like people do not need an ideology to think. If you doubt that, you have to doubt all mathematics that happened before late 19th century.
"They [logicians] realize that in order to talk of logic they don't need the full power of set theory, so they take logic as God-given instead." I do not know of any logicians, and I know many, who would say that logic is "God-given", or anything like that. I do not think logicians are born into a life rich with the "full power of set theory" which they throw away in order to become ascetic first-order logicians. That is a nice philosophical story detached from reality. The logicians I know are usually quite careful, skeptical, and inquisitive about foundational issues, reflect carefully on their own experiences, and almost never give you a straight answer when you ask "where does logic come from?" Your view is naive and inaccurate, if not slightly demeaning.
If I understand your question correctly, you are asking whether there is a difference between the following two views:
We start with naive set theory and on top of it we formalize set theory.
We start with first-order logic and immediately formalize set theory.
Well, we are proceeding from two different meta-theories. The first one allows us a wide spectrum of semantic methods. We can refer to "the standard model of Peano arithmetic" because we "believe in natural numbers", and we can invent Tarskian model theory without worrying where it came from.
The second method is more restricted. It will lead to syntactic and proof-theoretic methods, since the only thing we have given ourselves initially are syntactic in nature, namely first-order theories. There will be careful analysis of syntax. For advanced methods, however, we will typically resort to at least some amount of "naive mathematics". Ordinals will come into play, it will be hard to live without completeness theorems (which involve semantics), etc.
However, this is not how real life works. The dilemma you present is not really there. A working mathematician does not concern himself with these issues, anyhow, while a logician will likely refuse to be categorized as one or the other breed.
That is my guess, based on the experience that my fellow logicians are complicated animals and it is hard to get to the bottom of their foundational guts.
Let me address the updated version of your question.
There is a philosophical current running through parts of descriptive set theory, and this includes anything that might be described as classical real analysis, to the effect that the realm of Borel mathematics is comparatively immune to the chaos of independence. On this view, one regards the Borel functions, relations and objects as being the most explicitly given, and the land of the Borel is the land of explicit mathematics.
For example, an important emerging field is the theory of equivalence relations under Borel reducibility, arising out of the observation that many of the most natural equivalence relations arising in other parts of mathematics, such as isomorphism relations on classes of algebraic structures, turn out to be Borel equivalence relations on a standard Borel space. Set-theorists seek to understand the comparative difficulty of the corresponding classification problems for these relations by considering the relations under Borel reducibility. This concept provides us with a precise way to measure the comparative difficulty of two classification problems, which then assemble themselves into a complex hiearchy, increasingly revealed to us. To give one example, it falls out of this theory that there can be no Borel classification of the finitely generated groups up to isomorphism by means of countable objects (this relation is not "smooth").
This theory has been largely immune from the independence phenomenon, for several reasons. Perhaps the best explanation of this is the fact that Borel assertions have complexity $\Delta^1_1$, which lies below the Shoenfield absoluteness theorem.
Theorem(Shoenfield Absoluteness) Any statement of complexity $\Sigma^1_2$ is absolute between any two models of set theory with the same ordinals.
In particular, this implies that the method of forcing is completely unable to affect existence assertions about Borel objects, since such assertions would have complexity $\Sigma^1_1$, as well as more complex assertions. Because forcing is one of the principal tools by which set-theorists have come to exhibit independence, this means that Borel mathematics is completely immune from the forcing technology.
Furthermore, when there are sufficient large cardinals, then one can attain an even greater degree of absoluteness in various senses. For example, in the presence of large cardinals there are various strong senses in which the theory of $L(\mathbb{R})$ is invariant by forcing. Thus, even the realm of projective mathematics ($\Sigma^1_n$ for any $n$) is unaffected by forcing, when there are sufficient large cardinals.
At the same time, we know that it isn't strictly true even that Borel mathematics is immune from independence, since the $\Delta^1_1$ level of complexity includes all of arithmetic, which therefore admits the Gödel incompleteness phenomenon. But because the method of forcing is struck down, however, none of the more spectacular independence results in the realm of analysis, such as the independence results concerning CH and cardinal invariants, arise at the Borel level of complexity. Thus, I believe that the realm of Borel mathematics may be the best, although imperfect, answer to your updated question.
At the same time, it must be said that although the method of forcing is ruled out as a means of proving independence for Borel existence assertions, we have no meta-theorem that says that there will not be some future method that is able to establish independence for such assertions. Surely a major lesson of logic over the past century is the pervasiveness of the independence phenomenon, and I believe that it is only a matter of time for such methods to arise.
Best Answer
Caveat number 1: strictly speaking, no one actually works in the theory $T$, just as no one actually works in the theory $\mathsf{ZFC}$. Mathematicians work by means of carefully used natural language and not within a formal system. Formal systems are formulated as approximations that try to model what mathematicians actually do while at work. Now to address the question, with the above caveat in mind, are we always regarding every object as a set? Not necessarily always, just sometimes. The point is that $\mathsf{ZFC}$ and $T$ are bi-interpretable, so you can switch between both viewpoints at will without that changing the stuff that you can prove (and even better: both $T$ and $\mathsf{ZFC}$ are just approximations to what we actually do, so we can just do math as usual, and not worry about these nuances, and whatever it is that we're doing can in theory be translated to the formal system of your choice).