I have a strong sturdy fiber-blown fiberglass roof and still will never put un-necessary holes in your roof. Holes are where water comes in. No hole, no leak.
I use the flat/thin flexible 100w panels and tape them on with VHB tape. On a rubber roof I would remove any painted on coating to get to the actual material as the coatings could just peel off.
The reason to go with the flexible is that they are super thin and will not be hit by wind on the front side and also that you can lay a flat tape seam across the joint.
Yes, they are able to get more hot than the framed ones with air flow under, but so far this has not been a problem. Many weeks in summer desert temps and the panels still work.
Removing the tape is not that big of a deal if you have to take the panels off at the end of their life. A hair drier helps a lot, yet the tape will not let go at anything under 100mph (or more). I have not tried removing from a rubber roof though.
They are also a lot lighter, so less weight on the roof.
Alternatives would be to look for places where you already have screws or bolts going through the roof. Can you double up on these and put some custom brackets here?
On either side of the AC unit you could make some outrigger brackets using the AC bolts and 14 inch opening as the hold-down, but this would be very complex design.
Same for the roof vents…
Think outside the box.