That's just part of how Doom's map format works. No map editor can change that. But at least in SRB2DB2, you can draw the second FOF over the first without having the linedefs cross, because SRB2DB2 automatically inserts vertices wherever two linedefs cross.
Actually, with some work, it's possible to extend the map format and add a mode that works between SRB2CB and SRB2DB2 that separates FOFs into
layers which you could sort through in the 2D map editor, this could remove a lot of the confusion of where FOFs are on a map and might even make it possible to have a true 3D kind of map format -
Because FOFs could be created as sectors over another sector without any dependence on the bottom area.
Such a feature would have to be a CB only because we could optimize the game by
saving FOFs as part of the actual MAP format. That way the game doesn't have to go through the trouble of recalculating every FOF every frame(which would be a speedup for FOF-intense maps). And using an OpenGL system, this would mean even more speed gains as we could create OpenGL display lists/vertex buffer objects to make things run even faster
(and before any map extended is done, the game needs to add UDMF support too)
I've noticed that 514 - Water Current Slide (Without Jump) = Damage (Water) + Wind/Current. Now see, THZ1/THZ2's slime water with currents happen to use this exact combo, so...
Really? I didn't notice that, tell me if any other sector effect combinations are already used.
(By the way, I was sneaky - I added more sector effects by using slots that didn't seem to be used (like damage+exit sector))