The "avoid floors" idea, while interesting, may be a problem because SoftPlan is also trying to create a materials list, generate wall framing diagrams, etc..
An "avoid floors" tools would mess up the double top plate of the wall below, require a "portion" of the opening to be framed into the wall below, and wouldn't reflect how that situation would actually be framed (balloon frame the wall)...
And not really so much "avoid floor" (as there really won't be a floor there) as "multiple story window opening"
I think the framing of the opening in two separate walls would make this really complicated for SoftPlan... The wall below would need jack studs installed that would also be part of the wall framing above (how would that work?), double top plate framing would need to be broken / relocated, etc... I think it would be a mess IMHO...
But yes, it would be faster for just pure "modeling" without regard for the wall framing, or how it would really be constructed...