As I was trying to say, there is no reason other than that the file is simply new; I wouldn’t see anything inside. There’s nothing to change in the file - a new file will always be new (where “new” means “not previously seen on our userbase”).
The deep scan inspects the content, sure, but it doesn’t find anything wrong and doesn’t call your file malicious, does it?

Whitelisting a specific file may even be unnecessary - if the number of users of the application isn’t really small. As soon as the file starts spreading amongst various users, the file stops being “rare” and stops being deepscreened, automatically.

But the digital signature has the ability to prevent the special scanning pro-actively (because then the reputation of the digital signature “trumps” the reputation of the particular file).