This is how the Prime Directive works.
As the Federation makes certain technological leaps that redefine them as a people and separate them vastly/further from the younger species who have not figured out now simple technologies that it would be incredibly dangerous to share these advances with other space faring cultures because they would most likely do something stupid and get themselves killed or light up a crusade, it's the Federations responsibility to section themselves off from these younger races for their own protection.
I see transwarp and time travel as two bench marks which with the increasing sophistication of the federation will be means enough to seriously think about pairing down their list of friends and acquaintances who are too stupid to handle responsibly what the federation takes for granted.
With a big enough transwarp reactor they'll be able to shield off the entire federation like China did with that wall of theirs when they decided they were too cool for school.
With complete control of time they'll be able to physically remove the federation that it won't even be noticeable to the prying eyes of the filth and rabble still skirting around with "warp".