I installed the MaxxAir Fan/Mate. It installs about the same as the MaxxAir II. The clips will be sitting on top of the lap sealant around your vent so it won't likely actually touch the roof material. If you're concerned about the clips rubbing on something you could cover the lap sealant with Eternabond tape before installing the vent cover but I doubt that the clips would have any detrimental effect. Just check that the cover remains secure on the vent when you do your regular roof inspection.
I put the Eternabond tape over all the lap sealant on my roof as extra protection for the seams since the lap sealant tends to need frequent maintenance.
2011 Rockwood Signature Ultra Lite 8293SS, 12K Equal-i-zer
2016 Ford F-250 XLT SuperCrew, 6.2L, 4x4, 6'9" bed, 3.73
2010 Rockwood Roo 23SS (2012 - 2014)
2009 Ford F-150 XLT SuperCrew, 5.4L, 4x4, 5'6" bed (2012 - 2016)