Well I ended up finding some older cars and it looks like the situation is this.
The Modified AAR cars weren't deigned correctly to accommodate the same under frame as the regular 1937 cars even though that's what they use. Namely the center two cross members don't sit flush to the floor because the floor isn't notched out like the regular cars.
Basically, I believe every Modified car has a bowed center sil. This is something I'd like to prove or disprove. One easy way to tell is that the center two cross members stick out below the door tab. Also, the next cross members towards the ends aren't touching the floor so they can be pushed down/up.

Look below the door. You shouldn't be able to see the ends of the cross members if everything was flush.
I had a under frame I though might have been an earlier version but it look like it's just from the 12 panel box car. The 12 panel doesn't have the notches, but the under frame is designed to take care of that.
I'm going to see if I can get IM to fix this for the future along with maybe getting the 5/5 end from the 50' car to fit (many of the modified cars have the wrong ends even though IM makes them).
On the plus side, I didn't realize that IM went to etched metal running boards. They look real good.
Jason