If we are going by amenities and desirability, and not by attaching value to some vague "flagship" label, there is no good argument for the new rooms to settle at or below VGF points. I agree that they aren't likely to price these rooms higher than the coveted VGF, but the result is just going to chill the demand for VGF rooms in my opinion.
The new Poly rooms are a better location at a more immersive resort. If we can stay in one of those rooms, and get on and off the monorail before the VGF folks, walk to the TTC to go to EPCOT, and enjoy the whole Poly vibe (while still being able to walk or boat to VGF to get our fill of its ambiance), I'm not sure why we would use the same number or more points to stay at VGF -- unless we were either in love with the Beaches or Courtyard pools or really valued the mile-long walk to MK (which, yes, is still better than no ability to walk).
This does assume that the tower will be 100% part of the rest of the Poly resort and not subject to some restrictions on use of the resort (i.e., Lava pool -- I can't think of anything else that would matter). If tower guests can't use the Lava pool, and the tower pool is just meh, maybe that changes the calculus a little.
I say the same thing when comparing BWV and RIV too. I think they overpriced RIV relative to BWV, but they didn't really have an option because BWV was already long-established at such a value. I bet if they could erase the slate and start fresh with one of those Men in Black memory eraser things, they would price BWV at or above RIV. And I wonder if they'll avoid that same mistake again with Poly/VGF.
To be clear: we love VGF. We stay there often. This isn't meant to disparage VGF. It's just meant to compare the new Poly rooms to the next closest options.