Yeah java doesn’t need some weird installation, it’s actually pretty decent that as long as all it’s file are in a directory tree in the right paths then it all ‘just works’. 
If you’re still running it in a chroot then that would likely be why, it can’t access your main user theme information.
That’s just Minecraft’s normal scaling, can change that in options (from Auto to whatever you want, I personally use small, which is too small for most people but I like it, lol, I change it to the next one up when streaming though so people can see things).
Yep, it’s a weird integer scaling multiplier based on window size, it can definitely get larger than the largest prebuilt config, lol.