Makes no sonic difference. Keep them
Yes I changed bridges from 50mm to 53mm when I went to a pre-notched TonePros on my guitar with 50mm Warpigs and the spacing hasn't caused an issue yet. I guess where you might hear it is on the high E
The difference should be barely audible and certainly not hold you back in any way. If it helps, Eddie Van Halen's original guitar would have been the same way since he took a PAF from a Gibson and put it in his Frankenstrat.