Ah yes, I see your dilemma. It looks like applying for one or both of the birth certificates might be your only option. Assuming your William is definitely the one born in Maidstone (parents Alfred & Frances), the other William will presumably be the one born in Nettlestead (parents William & Elizabeth), whose baptism appears on familysearch.org on 9 Dec 1894, possibly implying his was the later birth.
Odd... you would think that an entry in a family bible was correct, so maybe this birth index entry *might* be the exception to the rule regarding registration quarters. It'd be interesting to find out. Sorry not to be able to help!