Can I re-enter Thailand for a 60 days visa exemption after leaving on a tourist visa, and what are the limits on travel if I have a work permit?

Yes, you can exit, re-enter, and get 60 days.

If you have a work permit by the time you leave, you'd be on a different visa that allows having a work permit also (most likely non-B). You can then indeed NOT just fly out and back, but you need a re-entry permit, as you need to keep your non-B active.

Q. would I be able to leave Thailand and then come back in for the 60 days visa exemption?

-> It's possible. Even after you apply for a 30-day tourism extension.

Q. if I have obtained a work permit by this time, are there limits on leaving/returning to Thailand?

-> That depends on the phase of in-country Non-B visa and extension applications. in most cases, you can travel out from/into Thailand with a valid re-entry permit as long as you get back to Thailand within the current stamp validity.