Manufacturer s product page for the braces.
How to attach pump jack to roof.
Make sure to line up the jack perfectly with the rafter with the bottom butt of the rafter visible at the roof edge.
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.
Attach two jacks to the roof by pulling up a tab of one of the shingles sliding the top of the jack under it.
As you noted the jack connections should be installed under the top layer of shingles.