No, they aren’t. If the ZWS039 isn’t available in 2.5.12, upgrading is the only way to get it.
Actually, it might not be as much effort as you think. You can still use text files for configuration, so you can just set up a new OH3, add bindings, and then copy over your items/rules/sitemaps/etc. You’ll just need to update the items to point at the new thing IDs and update some of the breaking changes in rules.
I’m not saying that it’s easy, just that it may be easier than you think. I’d suggest waiting until 3.3 releases next week.
No problem. So long as you clone and backup, there’s no reason to fear it since you can always fall back to what works.
You can try the in-place upgrade, but I personally think it’s better to just do a fresh install and move over your text files manually. Once it’s working, you can take your time moving items/rules into the UI, or just leave them as they are.