It's possible to get the overframing in this case, just takes tweaking the edges of the roof planes to get them into position. Usually when you run into the case of the shoe plates not generating, that means the edge of the roof plane isn't properly seated on the roof plane below it. What I do to get them seated properly is by selecting the edge of the overframed roof that I want a shoe plate along and use either the Place Roof Plane Intersection Point tool or Join Roof Planes tool.
The Place Roof Plane Intersection Point tool works some of the time, but with more complex situations it may not give the exact points I'm looking for. The Join Roof Planes tool works nearly all the time, but it does modify the lower roof plane's edge as well, so I have to move those edges back into place afterwards. It can be a bit tricky getting all the edges in place, but it is possible.
After poking around the plan for a bit, I noticed that the pitch of the truss bases didn't match the pitch of the lower roof. Changing the truss base's pitch to match the lower roof seemed to have fixed it, though I had to redraw the truss base on the right side of the building to get it to work.
mLongChief's post in Roof Over frame was marked as the answer