I haven't heard of "Through the Roof Sealant" so I can't advise you on it's use.
My tried and true method of repairing leaks is to remove the skylight, inspect it for cracks, and thoroughly clean the roof surface and the skylight of old caulk with methyl alcohol or acetone, whichever works better as a solvent.
Use putty tape or butyl tape on the skylight remove the paper backing and reinstall the skylight in the proper position.
I use one size larger diameter screws (#10 instead of #8) to insure a good bite into the fiberglass, longer screws really don't make any difference. If I can't use the one size larger screws, I'll mix some fiberglas resin/catalyst or bondo to fill the existing holes, let it cure and then pilot drill the holes with the right size drill.
Hand tighten the screws, power drivers are nice but it's very easy to overtighten and strip out the hole you just repaired.
Use Dicor self leveling sealant to seal the edges and screw heads.
I know this is more than you asked for, but I know for certain that this method works. Taking shortcuts on water leaks only means you get to do it over again sometime in the (near) future.
Denny, Connie & Shadow (former barn cat made good)
2006 Tiffin Phaeton, Cat C7, Freightliner Chassis