It likely boils down simply to "Everyone has their own idea that they want to add in as their own personal contribution, but it turns out it's all the same idea because no one does checks and balances on each other."
Right. Like... there needs to be someone going "oh you want to include a US government agency that works with or keeps tabs on the Transformers? We have this, you should use it."
Again, not the biggest fan of the Bayverse but it seems like the franchise could solidify some of its mythology if they went "ok Sector 7 is going to be our secret government agency, MECH is for human baddies," etc...
It's not that I want everything to be the same but like.... Batman is always being reinvented and re-interpreted but it's not like every new version of Batman comes up with a new GCPD commissioner that just has the same basic character and function as Gordon.
The franchise can both grow in new directions and solidify its mythos at the same time.
It's probably because nearly all of those agencies aren't terribly interesting in and of themselves. Sometimes you get an interesting character, like Silas, but overall, they're treated as interchangable because they basically are.
It's a self-fulfilling prophecy. The EDC, Sector 7, Skywatch, GHOST, UNIT-E, and MECH aren't terribly interesting on their own, which is why there's always a new org that basically does the same thing in the next revamp.
At the same time though, none of them will be interesting enough to build on if someone doesn't take the time to make one of them memorable enough to become a reoccurring element in the franchise.