Don't know how Crimson Echoes turns out, but one thing that CT shows, is that it's not exactly clear why Frog became human at the ending sequence in Trigger. It only happens if you kill Magus back in 12K BC, but then, it doesn't happen instantly.
I'd imagine that if he once had the power to change Glenn's form, he could do it again. But, Lavos sapped a lot of his powers in the battle. I think it would have been cool if Magus had a tech to make an enemy as a weaker form, as you could do in Secret of Mana. As we've seen int the banter in Echoes thus far, Magus definitely dislikes Glenn again, moreso than at the end of Trigger. Perhaps Magus' life was "bound" to Lavos somehow, and only changed from after Lavos died. Just speculation here.
