Honestly, what really breaks them is the 0% autonomy floor. If they kept the 75% autonomy from territories they'd still be worth it and also relatively balanced, even with the new buildings. Then they could have -50% Sailor/Tax/Manpower additive multipliers and let the new buildings make up for them. I mean, they'd clearly be still stronger than non-TC territories (+100% Production Efficiency, +30% Goods Produced and +100% Trade Power lmao), but we would not be in this mess.
Worth pointing out here, there is a government reform that reduces the autonomy floor to 10% in all territories. So the 0 LA floor for TCs is less important in most ways than the fact that they don't contribute to your territory corruption. Of course, beyond a certain point in a WC game, you're just going to have to live with being capped on that and so the marginal cost of adding more territories vanishes anyway. At that point a new territory with a 10 LA floor is actually going to significantly contribute to your economy, and that's to say nothing of all the manpower this opens up.
I'm thinking the way it will play out is that the reduced LA floor for territories will (more than) pay for the cost of having rooting out corruption permanently maxed and so the net of the changes will be a limit to how much OE you can run without accumulating corruption. Territory corruption maxes at 0.8, rooting gives a max of -1. If you add in ahead of time on admin/dip, 3 stab, and admin/defensive policy you can mitigate 1.26 corruption per year while accumulating 0.8 from territories. That would allow you to have an average of 92 OE and remain at 0 corruption. Adding in the Espionage ideas and policies increases that substantially.
Point is, we've all mostly been looking at these various changes one by one without enough consideration of how the combination will change the game. The manual's reveal that the relevant reform now reduces the LA floor to 10 rather than 50 is actually very significant.