Saw this a little late but while they’ve never straight out said they are using the “new” engine for GD2, you don’t need a calculator to reach the conclusion that it wouldn’t make much sense for them to invest the time and expense in rebuilding GD’s engine and not use it for that purpose.
It’s also noteworthy that recently one of the devs accounts on the FF Steam hub (I think it was medierra or an account under his control) mentioned that it was also being built with other game genres in mind as well. I need to find that post but I can’t remember where I read it off the top right now.
So it sounds to me they potentially have aspirations to eventually have their own custom company engine with which to build all their future games within. Will be interesting to see what comes of it.