In my opinion (for what it's worth) longer set is always better unless you are dealing with something that either can't be clamped or there is a risk of running or sagging. When dealing with wood, the longer it is on there before setting the deeper hold it gets in the grain.
I expect the "System 3 they are selling is West's System three epoxy" it's just a thinner grade of epoxy. For the most part the real difference in epoxy is in the curing rate and the thickness. There are some differences in UV resistance but epoxy is not very UV resistant in any form. That's why boat people use the above procedure to varnish their woodwork. The Spar varnish resists UV better than Epoxy.
As to the thickness, companies use fillers to increase thickness. Some use Talic and that not only is NOT waterproof but will absorb some water and make the joint or fill fall apart. Some use metal to make the fill harder for threading etc. If you ever want the strongest filler ever made, mix up a batch of West Epoxy, hold your breath and chop up some asbestos. The barbs that make it so bad for you also make it the strongest filler on earth. ....Gee, I'm going on.
OH to answer your question, use 90 minute or 120 if you can find it.