No, "User app" means code you've added yourself (under "Apps Code"). Rule 3.0 is closed source and would be a built-in app, but the only way to keep using it on new hub firmware is to have already had it installed, ideally with a "clone master" rule you could use to keep making new ones if you want. No way around that besides already having done so restoring an (entire) backup that had it.
That being said, its not getting any love anymore. It's different, and some things do take more clicks, but Rule 4.0 is the only one getting updates and new features. They've also hinted (in the last Hubitat Live episode) that RM is likely to stabilize here for a while with no major changes, so it's safe to learn without worrying that you'll have to change everything you know again. 
If you haven't seen the docs, there are lots of examples of how to rethink Rule 3.0 rules in Rule 4.0 terms. I understand the desire either way, but I think this is the best bet long term. Good luck with whatever path you choose!
