Actually, I just thought of the same idea today, except it would be more like a cave. One thing that Seasons has, that would certainly make a superdungeon like this possible, is that it contains an interaction similar to 12 00 that displays the dungeon name, but it works for stairs. A tower would be good, but I think a cave would make more sense since it's kind of strange to have a water dungeon about 4 floors up.
I'm also thinking too that the dungeons need not nessicarily be all "one dungeon per floor". I wager it's possible to have multiple dungeons on one standard dungeon floor. How about a tower, but there are dungeons above and below it. Water dungeons(as well as other liquid based dungeons), could be below the tower, while the rest could be above. Remember that just level 6 alone was actually quite tall for a dungeon. Of course dungeons are limited as to how many floors they can have, but it could work.
Also, you can configure the portal warps to warp to different levels, though it can't cross map groups. That means it could be possible to have warps from the bottom of the tower, to the top, or anywhere almost. I would hope that a megadungeon like this would require lots of backtracking and getting items in different orders. I mean who's to say that you shouldn't walk into level 7 with only 3 hearts and a power bracelet. You might not get far, but perhaps rewards for those who dare brave danges before their time are to be found. Gasha seeds could be retooled into somthing, like perhaps dungeon indepenant keys or somthing.
Well, this is more of a mini-hack with short "dungeons" that offer lots of action and challenges. I like to think of this as a boss run with an additional challenge, and in this hack, there's one part where it's really hard to get past without taking ~2 hearts of damage, even though it's only the 4th room you visit in the first floor.
