Yes you can't interact with Maelle afterwards but she will still be in your team, it will always be the first person to fight. I adapted my run to that. You get control of Maelle after Epilogue. so Final fight is still okay

I have not been able to wrong warp with flags specifically, curator skip works with the manor door, but I'm not sure about the esquie wrong warp and others. For old lumiere I found another way to skip by going out of bounds. Maybe there's a better way.