Or simply add the magic directly to calibre via a source checkout.
As I understand the main objection is that it would run contrary to peoples' expectations.
So if you, personally, want calibre to speculatively chmod fils before trying to add them, then you, personally, can tell calibre to do so.
But I would feel nervous about adding it upstream -- what, more options, and this one to do something that is inadvisable to begin with?
There is such thing as feature creep, and features designed for one specific user are feature creep. Besides, the existence of an option would encourage people to use it!