I have already addressed it for the next maintenance release but for now you need to rename FSX or FSP exe's. Am I right in thinking you only need to use the migration tool when adding scenery, etc? If so I guess it's not too much of a problem.
In theory, its mainly only needed for installing addons yes, but also adds numerous shortcuts into the P3D root folder. You're right though, that wouldn't actually stop us renaming or moving the fsx exe. Just means having to remember the opposite when using the tool;-)
Used PFE for years and love it. Havent yet taken the plunge for the PF3 registration, but I will. Too may addons and not enough money;-)