There shouldn't be any difference in this case between an extrude object or a generic solid, assuming they have "Merge with Structural Objects [...]" checkbox checked. I experimented a bit and was getting split lines in some cases but not others, though the fill was merged. (You can test that the fill has been merged by converting the viewport to a group, and checking if the fills inside the group that you expect to be combined are combined into a single polygon or polyline.)
The merging can't simply use our standard Add Surface code because the incoming objects might have different pens from each other, no pen on certain edges, or even different pens on different edges (such as the individual component polygons from a wall with components.) That's why if you do that conversion of the viewport to a group, you'll find the edges are separate objects from the fills, and they are always drawn on top of the fills. It looks like in certain cases edges that should have been removed because they would be covered by the fills are not, and then they're being drawn on top.
This should be reported as a bug if it hasn't already.