They'd be negligent not to ask for clarification, as clear as it seems now there was confusion and debate about all kinds of things. At different stages the green flag didn't exist, only applied to the pitlane, was photoshopped in and was considered secondary to the light.
I think you're being a bit naive here.
1) At the time they asked for clarification, the slowmotion footage clearly showing the green flag was widespread across the internet. If they saw the original youtube movie (that missed the green), surely they would have seen that slowmotion footage too.
2) As for the photoshopped part: they had access to the same material as that youtube poster - he just used images from the world feed. You're telling me they don't have anyone that knows how to take a video source and freeze to a few key frames?
3) "Was considered secondary to the light" - you can't possibly buy this, right? I'm pretty sure Ferrari has people who know the rules very well. No, scrap that, I doubt there's someone at Ferrari who DOESN'T know that flags are valid from where they are waved up until the following light board or marshall post.
I have no problem with Ferrari asking for clarification, any team can do so. But for me this was just averting the responsability: instead of them telling their fans it was OK, they let the FIA do it for them. Even after the FIA verification, Ferrari hasn't confirmed the pass was legal, they just said "we consider the matter closed". Because of this, heaps of Ferrari/Alonso fans are still convinced that the FIA covered up an illegal pass.