Hi, BruceMc here. The first thing I'd do is go look for other Winne units similar to your model. I'd be willing to bet you'll find several with bunks in the very same house as you have.
I've been around class C's for a long time, and I've never seen one that was structurally different if it was set up for an entertainment center than an overhead bunk.
If a manufacturer did this, they'd have two structure designs, which makes no sense from a manufacturing standpoint. Plus, that overhang has dynamic forces acting upon it while underway which probably equal or exceed any average person or couple in the overhead while the unit is at rest.
Even our old Four Winds, which is not known as a "quality" manufacturer (We manufacture value!) has welded square wall aluminum framing with formed foam sandwiched between the interior luan and the exterior luan/plastic siding. That alone gives the structure a lot of strength.
That all said, if your unit has a short overhead that is 2-3 feet long, it may not have the floor strength as it was never designed to have the bunk option, but then you'll find no others of that model line that have a bunk.
I based my decision on the fact that our new Sunseeker has 3 options for the overhead space as I mentioned in my original post:

Again, I'd search for similar models of the same brand to see if, indeed, there is bunk options. If so, I'd (kindly) suggest the Winnebago rep didn't know what they were talking about....
My $0.02 worth....