It's important to think about the order of events here, the order is not: Ferrari consider a protest, YouTube footage emerges, internet discussion generated, media reports on internet discussion and Ferrari's "protest", Ferrari sends letter, FIA responds, media updates story.
The actual order is: YouTube footage emerges, internet discussion generated, Ferrari consider their protest, media reports on internet discussion (but is behind the curve as usual) and Ferrari's possible protest, Ferrari sends letter, FIA responds, etc.
So what actually happened here is that Ferrari capitalised on a period of confusion among a lot of fans on the internet (not helped by most media outlets like the BBC not reporting the story accurately), decided to give it authority by writing a letter, and then refused to properly acknowledge the reply (knowing that plenty of their fans will continue to think the pass was illegal). Even other team bosses were reported to have seen the footage and agreed there was a green flag.
If you don't think that's what Ferrari did here (i.e. you think they actually needed clarification) then I think you also have to believe at least the following claims:
- That Ferrari didn't have people watching Vettel's onboard footage during the actual race looking for exactly this sort of infringement (and note how quickly they responded to the Kobayashi claim, as soon as it was put to them)
- That Ferrari couldn't have easily analysed the overtake themselves, once they became aware of it, as they lack the means to do so, which would require believing that they lack:
- the footage (widely available on the internet and no doubt Ferrari have/could access even better quality footage); a circuit map (also available on the internet if they don't have one handy); a copy of the rulebook explaining the flag/lights system (available on the FIA website).
Again, think about how quickly people were able to dismiss this claim on the internet by simply using the (limited) footage available, applying a small amount of logic and looking at the rulebook. Now consider why Ferrari couldn't do that with all of their understanding and resources, and most importantly, consider whether they had anything to gain from perpetuating the confusion and their relationship with Red Bull.
Lastly, the above being the case (and seems by far the most likely option) I don't see Alonso as being involved. If Ferrari didn't need a clarification as I suspect, then the move was just a political game and although Alonso is not adverse to the odd mind game and attempt to undermine Vettel's title/ability, he wouldn't have anything to gain here.