The problem you are facing is other overhauls maintain some compatibility through wryebash, since they edit spawning content or add new content they do so much to change geometry of the world or alter default areas in ways that would block other mods typically. What you have in mind would though, if you alter the physical structure of the vanilla dungeons or redirect them your mod will be incompatible with thousands of other mods. Take for instance Enhanced economy has merchant quest that send you to find items in many of the games default dungeons just to get players to explore more. Many mods add a unique weapon hidden in a dungeon somewhere. Many quest add new npcs or items to be found using some vanilla dungeons. All of these would be in conflict with any dungeon you alter too much or close off. Which is why I say you are better adding to instead of removing. I don't think there would be any problem adding some elements to the dungeons or altering decoration as long as the key features stay intact but I would think your safest way of overhauling dungeons is expand them in some manner. Let the vanilla part of the dungeon be just a mask for something you put in place deeper. I mean I don't think going into a normal looking for then taking a door that leads to another area in which a group of rebels have set up base with flags handing, weapon storages would be a big deal. I mean they would want to hide their operation in the fort not announce it to the world on the outside of the place.
Just offering some ideas here, along with what I offered before. You have to be careful how you approach this as too much changing could mean you will be one of the few using the mod because if it conflicts with ayleid steps, OOO. FCOM, enhanced economy, Starx vampires, and dozens of other quest and new item mods then not many people are going to look into it unless they just want to use it as a step toward something totally different like combining it with Warcry new dimension or something.