Can I use less-known (but defined) abbreviations in section titles to get rid of very long expanded titles?
As the author of the comment you cited, let me offer the following distinction: a thesis generally has a much smaller "reach" than a journal. I would let a graduate student get away with some things in a thesis that I wouldn't normally do in a journal article.

If you need to use the abbreviations to prevent things from getting unwieldy (many multiple-line section titles is getting unwieldy, in my opinion), then I would go ahead and do so. If any of the reviewers of your thesis has a philosophical objection to such a practice, you'll be sure to hear about it.