favored class is a social thing
It seems to me that favored class is a social thing, e.g. dwarves tend to become fighters because that's part of their culture. Indeed, all dwarves undergo that dodging-giants training anyway.
Someone raised as an elf would spend a century as a child playing with magical baubles and watching the adults perform amazing/beautiful feats of wizardry, hence, a tendency for all elves to view wizardry as a natural choice.
Halfling culture is about resourcefulness and resilience, hence the tendency toward roguishness. Half-orcs are mocked and picked on by whomever raises them, so they quickly learn to be the schoolyard bully...
Imagine if a dwarven fighter/wizard were reincarnated as a gnome. Why would his favored class suddenly become bard? This would be absurd; gnomes tend toward bards because they are chatty and gossipy and showy. Someone raised as a dwarf would continue to be gruff and standoffish, and would not suddenly feel the need to become a bard.
Swapping low-light vision and darkvision is easy. What about training? Would that dwarf-turned-gnome lose his stonecunning? That doesn't seem right. Would the elf-turned-halforc suddenly not know how to make boots of elvenkind?
Note that boots of elvenkind do not require the wearer to be an elf; they only require someone with the knowledge of an elf create them. I would say that a magic item that requires the user be an elf MUST be created by an elf.