I agree that trade companies badly need more restrictions. Two ideas:
1. Make the whole old world a TC region - i.e. allow African and Asian countries to have TCs in Europe
2. have TCs require the global trade institution - this would properly make them a thing for the second half of the game rather than a completely overpowered tool for early blobbing
Both ideas aren't thought through and probably come with drawbacks. The main point is: something should be done about TCs.
The fact that TCs currently are something of a loophole doesn't invalidate all other balance changes implemented to disincentivize blobbing.
I've been having fun playing Kilwa recently and was somewhat bummed out to not be able to make a Ibera trade company and a Britannia trade company. Alas, maybe someday. But, they should fix how trade works before they do that (or do it at the same time). It is patently ridiculous that Kilwa can't get gold fleets from Peru, Mexico, and Brazil just because they're "further up the trade stream" than the new world or something. It was particularly bad to not be able to bring Peruvian gold to Kilwa when I held the entire Indian and Pacific Oceans excepting a small portion of Russian coast and all of Japan. I can see the talk naval advisor:
"Sire, we've sailed around the globe."
King: "Great, now we can bring Peruvian gold to Kilwa, right?"
Advisor: "That hasn't been developed by the Swedes yet"
King: "What do the Swedes have to do with anything? Are they even free from Denmark yet?"