This dude is really like my little bro.
こいつはマジで弟 soa natural?

As you've said, "It doesn't mean he looks like his real brother". It also doesn't mean he think that the person is truly (literally) his younger brother, though that's listed as one meaning of マジで。

The word "like" is key, I think. If you had said,
"This dude is really my little bro(ther)", then I'd say there was an issue, but by adding in like (まるで), it makes it perfect, IMO.

BTW, "bro" tends to have taken on its own meaning beyond "brother", and is often used to mean, "friend", or just "guy" (dude).

"What's up, bro?" -- not referring to an actual brother.

個人的に
"This dude is really like my little brother" にするけど。