grammar - Meaning of 「という訳でもないのだが」

I have a question about the meaning of という訳でもないのだが in the following passage. If I'm understanding correctly 「いたからと言ってなんだ」 - 「居たからと言って何だ」 would translates something like - "even if he/she was, than what", however I can't quiet understand the whole sentence.

"Well, it's not that, (even if she was there, than what)." - fast translation.

・・・・・・それにしても、あの少女のことは綾奈も知らないのか。

先程はうまく説明できなかったが、目立つ、というより、不思議な感じがした。

まあ、いたからと言ってなんだ、という訳でもないのだが。

・・・・・・。

ちょっと後で後輩のやつにもメールで聞いてみるか。

・・・・・・本当に、いたからと言ってなんだ、というわけじゃ、ないんだけどな。

Context: The MC seems a strange girl. And now he's asking his friends if they have seen here before.

Answer

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  "～という訳ではない" is a common set phrase which corresponds to "That is not to say ～" or "That doesn't mean ～", referring to what was already stated. Using でもない instead of ではない adds "not in particular" or "not really" feelings to the sentence.

  
  


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  There is another common set phrase "だから何だ？" （or "だからどうした？"）, which means "so what?" It actually implies something negative -- "that's not important", "It doesn't matter", or "I don't care".

  
  

These by themselves are easy to you, aren't they?

In the sentence in question, I think you got the last half right. But maybe you read the first half of the sentence using the above knowledge, like "so what? she is not important". That would result in something like "That's not to say she is not important," or "she does matter to me," which did not match the context. (Of course, the guy who said this (twice) is actually very curious about the mysterious girl. But in that sentence, he is trying to deceive himself, saying he's not interested.)

If that's the case with you, let's stop interpreting this なんだ part as "so what?" This なんだ is not negative by itself, but should be interpreted as "it somehow matters" or "it's of some importance". The whole sentence can be understood as "That is not to say {if she was there, then it somehow matters to me}". Or to put it plainly, "I don't really care if she was there".

There are similar idioms, 「どうということはない」「どうという訳ではない」「なんということはない」「なんのことはない」, etc, all of which mean "nothing special", "doesn't matter", "it's a piece of cake", etc.