Hmm... Good questions. Having looked a small amount into how the game translates ROM map data into RAM map data, I would guess that tiles 00, 10, 20 and 30 have dummy palette assignments, and the use of one of those in ROM simply calls the appropriate 1x1 tiles when the map is being drawn into RAM. That's how it works for the "multi" tiles - "98 04" in ROM ends up getting written into RAM as "18 18 18 18 18."
If I can determine that I'm right about that, then the solution would simply be to make the 4x1 tiles inaccessible to the user in the editor (a big old X, or whatever), and have their implementation entirely behind the scenes.
I'll look into that. In a couple of days, though, I've got kind of a busy weekend ahead.