I came across this sentence today 「アンタの本音が何で、嬢ちゃんが何を伝えたいかは俺にはハッキリ分かったがなぁ……」and was thrown off by the double が. I think I understand it but it still kinda puzzled me for a bit. Can some clarify this?
So I think what is confusing you here is that you think 何で is "why". In this sentence it isn't. アンタの本音が何で is a separate clause where で is the continuative form of だ. So in no sense is there any kind of double が thing happening.
The structure is "X and Y are clearly known to me" where X is アンタの本音が何で and Y is 嬢ちゃんが何を伝えたい.
Putting it together you get:
What your true motive is, and what she wanted to convey, are clear to me.