epoxy is epoxy, there should be no difference in adhesion, but if unsure do a test. As for the scarf, you can go either way. Sometimes depending on the timber, you can glass first then fill, or fill then glass over. I am a fan of filling first, but if you aren't careful, you can sand into the timber creating high spots (epoxy filler), because the timber sands easier, so it becomes a chasing game. best to coat with epoxy and leave it to harden up before filling. Make sure that you have a wide fill over the scarf so that it will blend in. You can also do a fill, rough sand up, glass over, then finish off fairing. There is a danger that you may end up sanding off your glass this way! As for untreated ply - all marine grade ply is untreated, and you strictly should not use treated, as the chemicals used are not user friendly to epoxy. I am not saying it won't stick, it just wont be as good, also any screws, nails, bolts etc that are left in treated timber, might react and corrode.
use a long board to sand off!
les