It's not one less quest. It just changes the quest destination. If you explore every dungeon before doing some quests then that's you're problem
I think that's kind of the point of the question, and I don't really know what happens if that's the case. Maybe the game will start sending you to dungeons you explored a long time ago, after all, by then the place would likely have respawned, and if you're quest is to kill an enemy there or find someone who went missing there or something, it can still make sense if you justify it as the dungeon having new residents. Or maybe you just won't get any more Radiant Story quests that involve dungeons, that doesn't mean you can't get other kinds, after all, I doubt all Radiant Story quests send you to a dungeon, Bethesda likely used used that as one example of how Radiant Story works.
As to quest markers, I don't know, I don't think it's been said either way. But I suspect it will be in, as it seems to be the trend in games recently, but I don't know, nothing has really been said on the subject.
As to the length of the main quest, I don't see how you can say 20 hours is too short, that's longer than a lot of standalone games you'll play, and we're talking about just ONE questline here in a game that will also have faction quests and side quests, and in past games too the main quest has only been a small part of the overall game. As long as the rest of the game lasts long enough, I won't complain if the main story is "only" 20 hours.
As for the mods - I HATE when people start messing up an otherwise stellar game! I hate it! I want to play the game the devs created, a Fallout that's, y'know, a Fallout, no blue sky and green trees for instance. So I'll miss out on many mods, but damn, I simply can't play Morrowind without Connery's textures, Vurt's grass, MGE, better bodies, heads, the mod that lets you know which skills you've increased since your last leveling up and so forth... In the end of the day I can't play the game without 40+ mods, same goes for OB. God, I LOVE the TES mod community!
Then maybe don't download the mods that "mess up" the game? It's not that hard to do, in fact, it's easier to not download them than to download them...