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.
How to attach pump jack to roof.
Attach two jacks to the roof by pulling up a tab of one of the shingles sliding the top of the jack under it.
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.
Installation instructions pdf each brace is attached to the house at two points.
As you noted the jack connections should be installed under the top layer of shingles.