The one with a better deck wins. If a homebrew deck goes against a meta deck then it's likely the meta deck wins, but if you homebrew a deck with meta cards vs homebrewing without meta cards it comes down to how well the deck is built. A homebrew with all the meta cards but without any game plan or poor mana source distribution is going to do worse than a homebrew without meta cards, but with a clear plan and cards that support that plan.

People not building their own decks and instead just copying meta decks is another discussion.