As far as the "nonsensical" dungeons go, well, there has to be a compromise between "believability" and "fun to play in" as always. Sure, yes, absolutely right, there probably shouldn't be these 50 foot long corridors between sections. But, OTOH, if every dungeon turns into the initial encounter for WG4 Forgotten Temple of Tharizdun, where the entire dungeon rushes to the defense and, if the PC's are successful, the entire dungeon is more or less empty after that initial encounter, well, that gets old fast.
So, yeah, you should make the dungeon plausible. And, frankly, the players have to be on board. If the players are going to be asshats and pick nits about every dungeon, well, don't run dungeon crawls for them. It's just not going to be fun for anyone. At some point, again, there needs to be compromise.
It's very much like ship maps. If you look at most ship maps for D&D, they are WAYY too big. The Sea Ghost from Ghosts of Saltmarsh is about 3 times bigger than it should be. It's a 90 foot Hansa Cog, when Hansa cogs were usually about 30 feet long. It's MASSIVE. But, needs must when you're trying to run an adventure on the ship. If you actually have a realistically scaled sailing ship, it's almost impossible to run 5e combat on it. So, you have a choice - bigger ship or boring encounter.