I've played many FR guitars with both wide and narrow necks , and I have never thought of such a problem... Usualy the neck starts wider at the body , then goes narrower up to the nut , and both e-strings flow about the edge of the neck.
I think the problem might be the FR locking nut , but I believe there should be different sizes for different nut widths ... You should ask where you're gonna buy the neck if a similar one has been used successfully with a FR bridge before.