I ran into the same issue when mounting the mag antenna for my Cell Amp. What I did was I got a 4" x 4" piece of magnetic metal from Home Depot, just a plate for a electrical junction box if I remember correctly. I got some two sided 3M tape, the heavy duty stuff that is rubber in the middle, not the cheap stuff that has a foam layer in it. I used the 2 side tape to mount it to the rubber roof and then used Dicor LAP sealant around it. I did a write up that has pictures if you want to see the details...
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