Were Scotland to leave the United Kingdom, the Union Flag would not therefore need to be changed. (Although they might have to reconsider its name)
Regardless of its origins, the British flag has become a unitary symbol, in which the appearance of the whole outweighs the interpretation of the parts. The main criterion for any new design, in fact, should be that it looks essentially the same as the old one.
It would be nice to include Wales more conspicuously, but just having the black field of St. David seems quite appropriate.