First focus on workshops and manufactories elsewhere, but... Per point in base tax, Churches in TC regions are more valuable than non-state, non-TC churches.
The 0 autonomy applies to tax as well and the tax income modifiers are additive. The -100% modifier is completely negated by the +75% core and +25% city modifier, and there's no cultural penalty either, meaning the +40% from a church is all income.
There are plenty of high ADM TC provinces w/ grain where a church is actually better than a workshop (w/o a manu). With no GoodsProduced bonus in a price 2 province, you need 2x DIP vs. ADM for a workshop to be better. With +60% Goods, it comes down to 25% more DIP than ADM.
Of course, with the manufactory it adds +5 DIP in that calculation so you only need like a bit more dip than adm for the workshop to be better. And that's not counting the Trade benefit from manufactories, which is why TC+workshop+manu. is so OP.
In price 3 and up provinces, the benefit flips quickly to workshops and the standard advice. And considering there's usually at least somewhere else you can build (or delete a AI docks and build

) you see why you should focus on workshops/manus.
If you're not ultra-blobbing, have extra building slots in TC regions, and have filled out your manufacturies and workshops elsewhere, and don't need a higher forcelimit, go ahead a build a church.