Okay pls play a major or mid sized Catholic country or Sunni country. Inform me of how many times DOTF stopped your expansion.
If you are a Catholic country attacking a Sunni country or vice versa, you would have to contend with the enemy DOTF. And yes, the DOTF will be less threatening if you are a major or middle sized country because you are a major and middle sized country and not a much weaker minor, obviously.
I don't get why you keep bringing this back to Catholics though, if you are in the HRE and surrounded by Protestants, you are going to have to deal with diplomatic penalties with your neighbours including having to fight their DOTF if you stay Catholic.
Even if this system did seem to benefit Catholics or Sunni only like you contend essentially, I still don't see how that would be an issue because all religions in the game have a unique situation and a unique set of bonuses and part of picking a nation is accepting the benefits and costs of the religion of your country- there is no reason for there to be any parity here anymore than there is any reason to say it is unfair that Catholics don't get a discipline boost like Protestants and Orthodox do.
Basically everything you have been saying here boils down to "it is harder to expand as a minor nation with a heretic religion to your neighbours" and I don't see how that is a problem at all. Many of the other criticisms here of the DOTF have merit, but not that it adds difficulty for playthroughs that should be more difficult (such as starting as Montferrat on Hard, switching to Protestant and angering your neighbours and then blaming the game mechanics when France helps them clobber you, a tiny and unprotected nation that aggressed against them).