Are you talking about the front roof cap by the destination sign, as well as the rear window surround cap?
If so, both of those on a 4106's exterior
are made from steel, not aluminum.
caps in those areas are made from aluminum.
Are they structural? Good question, but, IMHO, based on the few thousand rivets GMC used to retain them, I suspect that they are to some degree. Reason I say this is because if you've ever sat in the back of the coach while it's going down the road (especially a rough one), you can see the chassis flexing. Between the steel outer and aluminum inner caps, I believe these help to keep the bus roofline "square" to the floorline. But I'm also not a structural engineer, so take that for what it's worth.
That being said, I have seen numerous GMCs that have reconfigured the interiors with wood in the areas you're talking about, but have no knowledge of how the work was done.
FWIW & HTH. . .