Don't know about the skylight but the roof on my Flagstaff does the same same thing. Was told by the dealer and on here that it was not a problem. For what it is worth, the loose areas seem to come and go depending on temperature. I figure as long as it is not a big flapping area and there are no holes it is good.
2001 Ford F250 7.3l converted to F350 specs
2014 Flagstaff 8528RKWS
2 - 2006 model year Border Collies