Well, being a roofer myself, I have a dish and an OTA tripod mounted on my new roof.
I'm not a shingle monkey, I'm a flat roof guy, I had one of our crews handle the job. I wasn't home when they did the roof.. They removed the mounts and replaced them.
They marked each foot location and replaced them in the same locations.
They pre-drilled through the shingles (careful not to drill through the deck) put a small spot of roofing cement UNDER the shingle and over the holes, and used pitch pads under each foot, then drove the lag bolts home.
If you use a quality roofer and not a jackleg you shouldn't have a problem.
BTW, the dish didn't need re-aligning, my signals were actually a bit higher when they were done.
I've said this many times when discussing roof mounts, Roof Cement is the answer, NOT Silicone.
Roof cement is available in standard caulk gun tubes, 1 gallon cans, 5 gallon buckets, and should be the only sealant (in addition to pitch pads) used to seal anything on a roof.