Tedious, huh? Tell me about it - I think I have something like 10 levels in some of my solids!
However, while I think I understand what you are after, I'm not quite sure if the tediousness should be extended to 2D-polylines. A Boolean chain (that's the tedious part) should be introduced and all of us doing simple 2D drafting would be seriously edit-challenged - with up to 10 levels to deal with.
Having said that, especially your points 1, 2, 4 and 5 are most valid.
EDIT
Oh bugga! I'm supposed to teach Am'rican Hist'ry and Practical Maths to avoid the wrath of newbies, ignoramuses and Western Australian carport extension designers...
Right-o, here we go: cover the offending hole with a polygon and say "Add surface" and presto, it's gone! That should be easy enough for all other mentioned groups than the Western Australians.