Can I use less-known (but defined) abbreviations in section titles to get rid of very long expanded titles? I'm in trouble with long section titles in my thesis. For example:
I have defined the following abbreviations in a special section before the table of content, i.e., all abbreviations have been already defined before their usage in the table of content:

CRS: Centralized Reconfiguration Supervisor
DRS: Decentralized Reconfiguration Supervisor
FP: Forcible Path

A section's title is supposed to be something like:
expanded form: Functional commutativity of centralized reconfiguration supervisor, decentralized reconfiguration supervisor, and forcible path
abbreviated form: Functional commutativity of CRS, DRS, and FP
Obviously, the expanded form is so clumsy, however, these abbreviations are not frequently used in the text as @aeismail noted here:

In general, the only abbreviations that should be used in &quot;headlines&quot; and titles are &quot;standard&quot; ones that are normally (or at least very frequently) written in their abbreviated form.

Put differently, these abbreviations are parts of my contribution, with which research community are not familiar.
Which option is the best practice?
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.