Laying the standard kit bridge with the Wilkinson and lining up the pickup hole shows that the kit bridge extends further backwards, so if anything, the problem would be worse with the original bridge compared to the Wilkinson
Wilkinson over the kit bridge:
Side-by-side:
The Wilkinson is actually original Fender specs as far as I can see, the kit bridge and scratchplate seem to be sized as per the Squier models