You misread, either we remove the two that we have, or, we add two more options that does the opposite.
With unnecessary options like these we either cater to all, or cater to none.
I think we're on the same line but to be sure, you mean that we could have either:
- Two "more X" options available, none checked by default
- Two "less X" options available, none checked by default (while the "more X" are invisible and switched by those less X)
?
Edit: Regarding passable mountains and religious disabling I play with none. I don't want units to be able to pass mountains without the mountaineering promotion as the whole point of mountains are to be natural barriers for units (I think/hope this is what that option does, as I'm capable of building improvements on mountains without the option). Religious disabling is a very crude module, and a poor attempt at balancing religions.
For Usable Moutains I think the disagreement comes from a misunderstanding on what it does... From what I've understood it allows to cross mountains after discovering the Mountaineering tech; earlier you can't cross or use them (at least that's how it seems to work when I use it). But you say that you can build improvements on the mountains without this option? What does this option do exactly?

If religious disabling doesn't work well, another path would be to make this option BETA and off (or even invisible and off) and adjust the bonus from religious buildings so that their most powerful effects only apply if they're your state religion (I haven't checked if it's easily doable in the XML) - thus you don't get say +200%

