Well if you're applying to a lab for a PhD, it's not like applying for a taught masters or undergraduate. They're not looking for you to be better than a certain benchmark - they're looking for you to be the single best candidate for a single place. So while it may help you if you get the Masters, there's no guarantee that it would then make you 'better' than the same candidates the next year, or that the following year there might be less competition and you might not have got the place without it.
(And I had to show transcripts for every university I applied to, even though I'd already graduated).