The main point is in balance, and such scenario you mention is unrealistic. If, say, religion, with 10-15 temples would provide income equal to some small-sized cities, how could any ruler ever bother to found religion, "recruit" enough priests and followers, just to ensure some modest funding? I cannot imagine that. It is intended for those who have no other mans except such one, and no-one who has much more efficient way to earn money would ever bother. Moreover, so much effort is needed that I truly don't believe anybody would found religion and do so much religious job just to take some moderate funds. Net income would be side-effect for those who are fully in religion anyhow, giving them some small power.
Not unrealistic at all. I've seen it. Religions are often founded for the sole purpose of supporting realms. And if that's not the original purpose, they often end up that way, too. And how do they recruit priests? It is quite often those doubled-up characters you mentioned earlier. Could religion be as efficient as realm taxes? Maybe not. But when your realm is already producing as much gold as it can, and you still need more, would you turn down an extra 1,000 gold a week, just because it's not as "efficient" as going out and conquering another city?
Current financial dependency simply renders religions unattractive.
To some people, yes, I agree. But then perhaps these people aren't cut out to play the religion game the way it is done in BattleMaster.
However, one of your quotes describes much: )...)that would let you move in, so long as you didn't cause trouble(...).
That is the point! If you are so sure that someone will not cause trouble, ever, because he is so weak and will never be able to become very influential, you are taking care to make eternal stall 
So, wait, you think that religions should be given so much power over the state that any newbie religion should be able to move into a realm against that realm's will, cause as much trouble as they want, and have the realm unable to kick them out without it causing major problems? That's simply ridiculous, and the argument holds absolutely no weight at all.
Again, i don't see it in practice after many, many months of silent checking. you either have net negative income because of too many buildings, or permanent loss of followers because of too little buildings. maybe there is some difference to that when some religion totally prevails in wide area, which is the case only with some large theocracies, so you have your balance when you actually don't needed as everything is in your hands anyhow 
How many times do I have to say it?
It is intentional that religions are not self-sustaining in gold flow without noble sponsors.RTO's does not work without large addition support of courtiers, police-work etc.. which you will not get if you are not tool of mundane powers.
This is not correct. I have seen RTOs done by lone priests, or priests with little support.
But even with that ignored, you are again contradicting yourself. You've already complained that priests are relegated to auxiliary attachments to the army. So, you're an attachment to the army. That means you have the support you're just complaining that you can't work without.
in general that is ok that region needs different kinds of work to be maintained, but than it should be distributed fairly. with all priest powers i had, i tried to prepare region with about 600 population and lowest stats, to raise morale and loyalty before rto, to have it stable after rto, but did not manage it with rl 6 months of attempts, region that is outside of any route.
if you cannot use your highest power for even such insignificant region, than you really cannot create alternative way.
Then maybe something was working against you, and you should have given up long before that. These results are so far outside of any that I've seen or heard of that I can't credit it as typical, or even a bit out of the ordinary, without thinking there has to be some serious things working against you.
on the other hand, if we would want fair balance, than pagan peasants should make more troubles.
I'm sorry, but that makes no sense whatsoever. Pagan does not mean "atheist without religion". It means they don't follow an official game-mechanics-sanctioned organized religion. There is no way that I would ever support a change.
