I think the further away you get from anything being in its original context you risk the chance for it to be watered down. Karate has a lot of factions, federations, associations etc. I'm not sure about TKD, I have zero experience with it.
When people become the heads of these groups and they determine that they want to implement their own ideologies you run the risk of it losing its original essence, and purity. Judo is an example of a martial art that seems to be very well centrally governed compared to most others.
I'm always hearing about local bjj gyms cutting their affiliations, and going independent. If they're operating largely as an independent gym who knows what is being taught there? The guy who the gym got its name from may come around what, once maybe twice a year? That is if they remain under him to begin with.
If BJJ gets watered down I feel it is largely on the instructors, and the named persons in the community because they are supposed to be the "heads of the household". I don't think it can ever become a TMA. I think for something to be a TMA it has to be originally from Asia. I could be mistaken in that thought process, but I think TMAs are all Asian in origin. BJJ as we tend to think of it is not.