"I heard they do almost the same stuff"
Ermm not quite. According to the info, FOOK (for now) makes some bug fixes and some changes to vanilla nomenclature that they feel are better (which I agree with in some cases). FOOK also adds some items that were unused but were in the data, to some chests at the start of the game. (Edit: read the readme, it does some other stuff too ie. it ports over some icons for the various types of junk that a fellow made for FO3)
The compilation patch makes vanilla bugfixes. It includes the ones from FOOK plus quite a few more. Whether it includes any of FOOK's other changes that aren't quite bugfixes I'm not sure, it isn't clearly stated.
For that reason I'm currently running the community patch on top of FOOK.