Emily, that's an interesting (dare I say pithy?) theory and one I will ponder. It does ring a bell of familiarity. But if you are right, why don't crossdressers report (for example) phantom itching or sensation where a breast should be? When my nipple itches it's my real nipple, not the artificial one a couple of inches away, even though that's what I see.

It seems to me that phantom sensations come from where tissue used to be, not where it was "supposed" to be.