The room might not be style-appropriate for traditional colonial crown molding. But I have seen rooms with a thin band of material placed where the wall meets the ceiling.

If you did the thin band, maybe an inch high, then you could stop it at the windows and paint the thin sections of wall above the windows to match the molding.

If it were my house, I would skip the crown molding, skip the ceiling tile, and spend my time and money getting the popcorn off the ceiling.

I'd consider a cove molding instead of a crown.... and even then it might not work.

Once you add the decorative tile, you will likely be right at the window level - no way to do it and not make it look odd, imo.

I agree that the smarter move would be remove the popcorn and skip the moulding. It looks like you have beadboard on the walls for interest already. I would paint the ceiling the same color as the upper walls to make your eye look past the odd spacing. Not every design idea or concept works in every room.