Andie - My thoughts:

I never heard of return plumbing being "under the pool", but I suppose anything is possible. It is certainly under the pool decking.

Returns are usually opposite the skimmer (not near it) for efficient skimming.

A second leak is depressing, but possible if insufficient winterization was the problem.

A second opinion would definitely be desireable since you are looking at a bunch of money, but small towns can be difficult in that regard and time is of the essence since the leak is significant.

Given what my pool cost to build, $3,000 does not sound unreasonable to me if they do a good job.

Good luck,
~Rick~