NB, I would definitely not fall into the category “knows much about” in case of TitaniumBackup! I’m a total newbie to Android, and to TitaniumBackup. But of course I had a look at that that when moving to a unified partition.
Short answer to the title question: yes, TB can restore your stuff after a unified storage update.
Long answer: I did that, and it worked. I remember some hiccups, but can’t remember specifics. (Damn it, I should have documented this as a tutorial. Thinking about doing that when I upgrade from 1.6. to 1.8.5 for my bitter-sweet caffeine boost.) Anyway, I still have the first text messages received with my FP, dating to Feb. 2014, in the Messages app. I later replaced this app by TextSecure, which completely bypasses the Messages app and stores the texts in an encrypted database (and can be used as a messenger similar to Threema, but being open source \o/ and less intuitive /o\ than the latter). This app also retained it’s complete messaging history after restoring with TitaniumBackup.
FTR, since I had to change my mainboard, and re-run the unified storage update, this should be of particular interest for people who want to switch to other phones - or from another phone to a Fairphone.
Also FTR, I still find the backup/restore process with TitaniumBackup a bit… unintuitive, lest to say: clunky. And up until now, I could not get the “update.zip” solution of TitaniumBackup Pro up and running, which would allow you to restore the app itself without access to the Google Play store (which would be really great after an update, because I would not even have to look up my not-onscreen-keyboard-friendly WiFi PW, and could do all the restoring e.g. on a boring and long train ride).
Last, but not least, I would always suggest to do multiple backups with different offered solutions. Don’t put all your eggs in one basket - it’s better safe than sorry. (Oi, that’s enough proverbial safety lines for one day, isn’t it?)