There shouldn't be any difference UNLESS the individual coils have different characteristics to them.
For example, the Dimarzio Tonezone, which I have, the coil with the flathead screws sound sharper and more powerful than the other coil with the flat magnets, which sound warmer and lower output. So based on that, if I installed the TZ in the Bridge with either side nearer to the Bridge, I can expect slightly different tones.
peter green's les paul has the neck humbucker installed upside down. quoting from an issue of guitar techniques magazine, the article says it does not affect the sound. hmm...
i've tried it before on mi old les paul, sounds different, the sound is how should i say...less focussed? its more like a bridge pickup to neck pickup, and from neck pickup to floppier neck pickup, noe wad i mean?