I installed Yakima tracks on my PH roof a while back......I attempted to get the holes outside of the canvas but found that the tracks would be way out toward the edge of the roof...and as mentioned the roof gets skinnier at the rear, which makes things even trickier.
Since the PH top was off and headliner was out I just located the tracks where I wanted them and drilled..and used sealing washers with the fasteners. It's been a few years, no leaks.
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2008 E350 RB passenger 4WD SMB penthouse
2013 KTM 350 EXC
2008 KTM 250 XCF-W
2003 Honda Element
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