Because if it wasn't flipped, the tubes would be sticking up thru the top of the combo.
Lots of amps are designed like this. Where the entire chassis is just one piece. For the head, the tubes stick upwards from the chassis. And instead of re-engineering another version of it for the combo so that the knob layout can be identical, they just flip the chassis over, have the tubes hang down, and reverse the knob layout.
I do wonder why they chose to have the tubes stick up in the head, since in the mod50, they hang down just like in a combo. Probably something to do with fitting stuff in.