I don't think Firefox ever touches your user.js, I've never seen that happen or anyone complaining about it. And then it overrides prefs.js generated settings. The only time I encountered problems was with a big update failing to replace a couple of prefs.js entries, and it was some really obscure settings.
I dont think this is correct. I added the boolean security.ssl.disable_session_identifiers set to true in Firefox 62.0.3 and ran the SSL Labs browser test here: https://www.ssllabs.com/ssltest/viewMyClient.html. With the boolean set to true, Session Tickts under the Protocol Details section says false. Toggling the setting back to false and rerunning the set showed Session Tickets Yes. So perhaps you had a typo in the seeting name?