I think she's going to be doing something with 3D and using her indie stuff to develop/fund it. It's the only thing that makes sense at this point, and there IS a market for it. Filian has based her entire channel off of Mocopi capture, for example. Cover simply does not have the time or resources to invest into large-scale development of true 3D tracking on a daily basis, their studio is overbooked as is. I'd bet one of Ame's cards for negotiating the soft graduation was Cover getting first dibs on anything she figures out that can push the 3D envelope further. Cover essentially subsidizes their costs on development by making Ame an independent 3D contractor in the States, while also maintaining merchandising rights to the Watson IP; Ame gets the green light to pursue her passion projects without JP red tape and a way to rejoin the company proper if she needs to.
Now that it is clear that she's raring to go as an indie, I feel much better about her leaving. I'd even be willing to bet that Cover wanted to make it work with Ame without "graduating" her, but some fine print in Hololive's talent contracts was preventing both sides from being able to continue in the way they had been. Maybe something about ownership rights of intellectual property used or created on stream by a talent? Cover would NOT bend that rule in a conventional contract structure, it might make potential problems for them with other talents down the line.
I'm actually kind of looking forward to seeing what happens now.