I imagine FWF work involving penetrations and the like being a little easier without the skins on. But it seems like that would be before you get past the upside-down on a jig stage which doesn't make sense? I don't know, it was a long time ago for me, but I do remember that it's relatively simple to put the mount on / take it off while you work on FWF stuff; you may do that a few times before final engine hang etc. anyway.
I did all the FWF before the wings since I was working in a single car garage - the wings only went on once I got it out to a hangar a few months before first flight. I'm not sure why the instructions would say to do otherwise, maybe it's more about the -6A types?
A slight tangent here - if you have an old engine mount make sure it has the reinforcing gusset mod at the gear leg bottom intersections, or if not get that added. Pain in the butt since there's stripping and re-painting to be done, but way easier now than after cracks develop (ask me how I know / see pic).