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.
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?