No, it is not possible. It is consistent with ZF without choice that
the reals are the countable union of countable sets. (*)
From this it follows that all sets of reals are Borel. Of course, the "axiom" (*) makes it impossible to do any analysis. As soon as one allows the bit of choice that it is typically used to set up classical analysis as one is used to (mostly countable choice, but DC seems needed for Radon-Nikodym), one can implement the arguments needed to show
(**) The usual hierarchy of Borel sets (obtained by first taking open sets, then complements, then countable unions of these, then complements, etc) does not terminate before stage $\omega_1$ (this is a kind of diagonal argument).
Logicians call the sets obtained this way $\Delta^1_1$. They are in general a subcollection of the Borel sets. To show that they are all the Borel sets requires a bit of choice (One needs that $\omega_1$ is regular).
There is actually a nice result of Suslin relevant here. He proved that the Borel sets are precisely the $\Delta^1_1$ sets: These are the sets that are simultaneously the continuous image of a Borel set ($\Sigma^1_1$ sets), and the complement of such a set ($\Pi^1_1$ sets).
That there are $\Pi^1_1$ sets that are not $\Delta^1_1$ (and therefore, via a bit of choice, not Borel) is again a result of Suslin. He also showed that any $\Sigma^1_1$ set is either countable, or contains a copy of Cantor's set and therefore has the same size as the reals. His example of a $\Sigma^1_1$ not $\Delta^1_1$ set uses logic (a bit of effective descriptive set theory), and nowadays is more common to use the example of the $\Pi^1_1$ set WO mentioned by Joel, which is not $\Delta^1_1$ by what logicians call a boundedness argument.
A nice reference for some of these issues is the book Mansfield-Weitkamp, Recursive Aspects of Descriptive Set Theory, Oxford University Press, Oxford (1985).
The answer to your second question is yes. Let $G=(\mathbb{Q}[\sqrt{2}], +).$ This is a countable abelian group, so $\mathbb{R}/G$ is a hyperfinite Borel equivalence relation. In particular, it embeds into $\mathbb{R}/\mathbb{Q}.$ (See section 7 here for a summary of these results: Kechris - The theory of countable Borel equivalence relations, preliminary version May 8, 2019). Thus we can use a transversal for the latter to construct a transversal for the former. Let $X$ be a transversal for $\mathbb{R}/G.$
Let $V=\{(x + q\sqrt{2}) \text{ mod 1}: x \in X, q \in \mathbb{Q}\} \subset [0, 1).$ This is a Vitali set closed under translation by $\mathbb{Q}\sqrt{2}.$ We will show its outer measure is at least $\frac{1}{4}$ (in fact, the argument can be extended to show its outer measure is 1). Suppose towards contradiction that $U$ is an open cover of $V$ with measure less than $\frac{1}{4}.$ For each $n \ge 2,$ we can canonically find an open cover of $V \cap [0, \frac{\sqrt{2}}{n}]$ of measure less than $\frac{\sqrt{2}}{2n}$ by considering the least $m$ such that $\lambda(U \cap [\frac{m\sqrt{2}}{n},\frac{(m+1)\sqrt{2}}{n}])<\frac{\sqrt{2}}{2n}.$ With this we can recursively construct open covers $U_n$ of $V$ of measure less than $2^{-n-2}.$ Letting $\{q_n\}$ enumerate the rationals, we see $\{q_n+U_n\}$ covers $\mathbb{R},$ so $\lambda^*(\mathbb{R}) < 1,$ contradiction.
Also, here's an observation relevant to your first question. If $\mathbb{R}=\bigcup_{n<\omega} X_n$ is a countable union of countable sets, then there is a null subset of $[0, 1]$ which meets every mod $\mathbb{Q}$ class, namely $W=\bigcup_{n<\omega} \{x \in [0, 2^{-n}]: \exists q \in \mathbb{Q} (x+q \in X_n)\}.$ This is null since it countable outside of any $[0, \epsilon].$ Furthermore, if there is a Vitali set, that could be used to separate out a Vitali subset of $W,$ so a model satisfying these two properties would be a counterexample to the first question.
Best Answer
For instance let $f:[0,1]\to[0,1]$ be the Cantor function and define $g(x):=x+f(x)$. Then $g:[0,1]\to[0,2]$ is a homeomorphism that maps the complement of the Cantor set $C$ onto a measure one open set of $[0,2]$ (just because $g'(x)=1$ on $[0,1]\setminus C$). So $g_{|C}:C\to g(C)$ is a homeomorphism of the Cantor set onto a compact set of measure one, and if $W$ is any non-measurable subset of $g(C)$, $g$ is also a homeomorphism between the Lebesgue measurable null-set $g^{-1}(W)$ and $W$.
edit. As to the issue of finding a non-measurable subset within a Lebesgue measurable set of positive measure $S$, there is such a set of the form $S\cap (V+q)$, the trace on $S$ of a suitable translation of the Vitali set $V$. Indeed, the Vitali set $V$ does not contain any measurable subset of positive measure (reason: if $E\subset V$ then $E-E \subset V-V\subset \big(\mathbb{R}\setminus\mathbb{Q}\big)\cup \{0 \}$, while $E-E$ is always a nbd of zero for any measurable set of positive measure $E$). On the other hand, the sets $S\cap (V+q)$ for $q\in\mathbb{Q}$ are a countable cover of $S$, so one of them has positive exterior measure.