I was playing with both Factorissimo2 and Editor Extensions enabled. In EE's map editor mode, while on the default surface, I accidentally deleted a factory building while using the deconstruction planner (which, in map editor mode, completely deletes things rather than placing them back in inventory). This left the factory's unique surface (#11 in this case) in the surfaces list, inaccessible to regular play. Attempting to delete the unused surface in the map editor results in a crash.

Yes, that's intentional. Factorissimo2 won't just delete its surfaces because they are part of a surface pool that is reused after every 100 factory buildings by default (new factory building interiors will be placed at an offset on existing surfaces). This is a legacy feature: at the time Factorissimo2 was written, there was a hard limit of 255 factory buildings in Factorio because the devs didn't want too many surfaces.

Is there any way to make a new factory building use the orphaned factory floor?

You can place a bunch of factory buildings until the floor surfaces are reused, but I don't think that's what you're looking for. Is it somehow bad to just have the factory floor hanging out in the save?

Not especially essential, but it seems vaguely wasteful to me. Oh well, thanks for the replies!