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Absolutely, auto-adding is already pretty magical (particularly on windows, with its crazy file locking semantics) -- however, the solution to something being magical is not to add more magic to it, it is to remove as much magic as is possible. Read the code for the calibre auto-adder and you will find that > 75% of it is to deal with problems like antivirus locking files, or files that are partial because they are in the process of being transferred from a slow source, such as a network. That is all work calibre does to make the process as predictable as possible, given the inherent limitations of filesystems and OSes. Speculatively chmoding files before trying to add them absolutely will not increase that predictability.
And yes, as davidfor points out, file permissions can be a signal just as much as they can be noise. I have to agree with him that having an application simply override file permissions is disconcerting to say the least.
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