I begin by trying also to answer your question:
Why would we exclude $a$ such that $\gcd(a, n) = 1$ when the test works well without such condition? If we know that $\gcd(a, n) \not= 1$, we already that $n$ is not prime, thus the test is pointless.
The answer is that we are not excluding those $a$, but the chances of randomly getting a Fermat witness $a$ such that $\gcd(a,n)>1$ may be extremely low. At least it can easily be too low to help us in the task of primality testing.
On with my more verbose rant.
I am not an expert on primality testing, but I think $561$ is too small to truly bring to light the risks of primality testing by crude Little Fermat. After all, $3$ is a small number, and you are likely to hit a multiple of three sooner rather than later. But what if you stumble upon a Carmichael number with only relatively large prime factors (for the purposes of crypto we are talking 100+ digit prime number candidates after all).
For example, by Chernik's result if $6k+1,12k+1$ and $18k+1$ are all primes, then their product $n$ is a Carmichael number. If here all those three primes have about 40 digits, then the probability that any given Fermat witness says "Possible prime" is $1-10^{-40}$ or thereabouts - not good when the number to be tested is actually composite!
But, if you use a slightly more sophisticated witness based primality testing, such as Rabin-Miller, then you never have this problem. Each (R-M) witness yelling "Possible prime!" lowers the odds of your candidate still being a composite by a known minimum factor (IIRC the factor is four - but do check your sources on Rabin-Miller).
So the point is that due to the existence of Carmichael numbers we need to use something other than basic Little Fermat to get something like 99.99% certainty of the candidate being a prime with a reasonable amount of testing
(when 8 R-M witnesses, each cutting the chance of a false positive by a factor of four, will do it).
If the number to be tested would be a Carmichael number, then I'm not aware of any number $\epsilon>0$ such that each witness would lower the probability of a false positive by $(1-\epsilon)$. Furthermore (see the Wikipedia page I linked to earlier), there are quite a few Carmichael numbers in a given range. True, they form a tiny fraction, but when Rabin-Miller gives us the kind of a guarantee that Fermat cannot with the same computational complexity, why use Little Fermat?
The weak Fermat-pseudoprime-test is a good start, but there are infinite many composite numbers passing the test for every base coprime to the number, namely the Carmichael numbers.
However, if your number is large (say $100$ digits or more), and if it is a "random number" (no special form) and you choose a random base, the probability that the number is prime is already very high if the number passes the test.
The strong-Fermat-pseudoprime-test is much better. If a number passes the test with $N$ random bases, the probability that it is a composite number is at most $(\frac{1}{4})^N$. If the number fails the test, it must be composite.
If you want to be absolutely sure that a number is prime, either use the Adleman-Pomerance-Rumely-test (APR) or Elliptic-Curve-Primality-Proving. The APR-test is implemented in most programs with long-integer-arithmetic, for example in PARI/GP.
Best Answer
The answer to your question is "no", since obviously we don't get anything from $\gcd(b_{(i+1)-1}-1, n)$ $= \gcd(b_{i}-1, n)$ $ = \gcd(1-1, n)$ $= \gcd(0, n)$ $ =n$.
You have a small omission and an error in your description of the Miller-Rabin test: