Churches shouldn't pay taxes, but yeah, having the government collect the tithe seems like not enough separation between church/state. Even still, as long as the tax isn't compulsory for non-believers and the countries in question are generally happy with it, it doesn't seem like a very big deal.

FWIW, in the US and elsewhere, we have ideologies like Critical Race Theory which are not discernibly different from religions (certainly more religion than sociology or research) and which are taxpayer funded. (And no, this is not the same thing as religious studies programs--studying a religion/ideology is not the same thing as promoting, producing, and enforcing it).