I think that village will fit the rebuilded spire after the main story of FR is finished!
And therein lies the problem - the village isn't supposed to be suppressed until someone rebuilds the tower. It's just there.
From a purely technical standpoint, a patch would be a serious pain. It's not just a matter of making the landscape and path grids right. That's easy. It's overcoming the fact that FR didn't bother to make sure the formIDs were stable. TES4Edit already caught two errors based on formID clashes which would lead to game crashes if ignored.
There's also serious story and lore related clashes that a patch would be unable to resolve. The village has no expectation of another village being present (sure looks like FR added one to me) and I doubt very much the flow of FR is expecting an unrelated village full of people to show up at the base of the tower who are billed as caretatkers for the place.
Compounding things is the fact that I wedged FV into place to fit with UL:Snowdale without requiring a patch. The last thing I want to be messing with at this point are complex purpose patches to resolve conflicts of that nature. I'd much rather be spending my time on furthering other projects that have been in the pipeline for awhile and need some love and attention.
All too often people just want the land smoothed. All too often this is only half the job, or possibly even only a third of it. I'm aware that the audience will be more limited than usual. I was prepared for that simply because this requires a DLC.