FileBot

Instead of running the shell command from code and dealing with that,
is there a way to instead use Filebot as a library that integrates directly
with the code?

Since it is written in Java (I think), can it be used as a library there?

I have found noe Python library but it just encapsulates a few of the command
line commands and options and runs them in a shell in the background

(like any other programming langauge can do)

FileBot can't really be used as a library. If you're keen on C# or Python then your only viable option is using the filebot command-line tool. However, you can run custom Groovy scripts with FileBot and in that context there are FileBot-specific Groovy extensions.