They both seem to share a lot of resemblance with each other, the only major difference is that the doors light up yellow, instead of blue. Is this supposed to be a sign of something? Things to come, maybe?

Is there a question here somewhere?

There is now.

There are two reasons they're very similar, visually:

Realistically and technically: The Enclave tile sets were readily available to use. They look high-tech and spartan already, why not re-use them for a high-tech and spartan organization? Especially since there's a whole two places in the game where there'd need to be such a tile set used.

In story/setting terms: The Enclave tile set represents pre-war military bunkers, not necessarily Enclave built or controlled ones. The idea is to make them look so advanced that they're almost alien compared to everything else because they're so far ahead technologically compared to the rest of the wasteland. So the Brotherhood isn't 'turning into' the Enclave so much as occupying the same kind of high-tech military bases that the Enclave did.