Shouldn't be a problem, as currently, the editor doesn't stop you from putting anything anywhere.... I'd say that to keep from having to change the editor to allow custom wallsets on the floor too.
Okay, so, first huge thanks to Sophia and Joramund for the alternate tileset. I've got the basics in the editor (and discovered something I hadn't really thought about - you can't tell the editor on which side of the wall to "paint" the wallset while you're painting, so you have to go back and move them to the correct side. It defaults to 'CENTER' right now, 'cause I'm going to assume that that's what people will usually want.)
But I discovered what I think is a bug. Here's the level map:
Map of level
Basically, just a dungeon corridor to a sort of indoor garden thing. The purplish tint on the sides of the walls (and the entire wall tiles in the center) are the custom wallset.
The graphic glitch occurs when walking along an alternate wallset, on the right side, for the square the party is standing on.
Two screenshots, one taken while walking outside the 'garden', and one inside...
Outside
Inside
I think what's occuring is the wall gets flipped - its drawing the wall from the other side of the tile. Because this map:
Map of level 2
when you're walking along the side of the garden with wallsets on both sides, doesn't glitch.
*Edit*
Just to note, those screens were taken from DSB .20.