Future Black Ghost has probably fallen off the Evil Overlord Ladder, probably because someone (Sovereign/Baelheit) managed to wrest control of TRIDENT from underneath him. He has now gone back to his roots as the vigilante Skull Man and is basically acting as the bitter angry uncle of the future heroes. I'm not planning on him going to the past currently but he'll certainly be around for Phase 2

What Magnus is up to depends entirely on what the Autobots have planned and what his relationship with Arcee Prime is cause they didn't exactly have a great rapport last time she was in command.