Make sure to line up the jack perfectly with the rafter with the bottom butt of the rafter visible at the roof edge.
How to attach pump jack to roof.
Installation instructions pdf each brace is attached to the house at two points.
For the repair they should not be using clear silicone caulk the same stuff the put around the windows they should be using something that is approved for use on roofing tar or roof sealant.
As you noted the jack connections should be installed under the top layer of shingles.
The pump jacks ride on wooden poles which have to be attached to the side of the house by steel braces at intervals of not less than ten feet.