We didn't have this problem when we applied for Shey's passport even though her British nationilation certificate was in her previous married name and her British passport was in her maiden name.
From memory we just sent the certificate and not her Filipino passort with a covering witnessed solicitors letter stating that she had reverted back to her maiden name for all legal purposes.
I'll dig out all the relevant paperwork when we get back home and update. Hopefully it may be of some use