This is something I expected to cause hard-to-diagnose problems. Luckily, the most common way I'd change files inadvertently (git checkout branchname) does not use the time from the commit.
I would expect that the md5sum of a file is reasonably fast, and could be stored in the .zwc for sanity checking, instead of just the "newer than" check.
> Again you're unlikely to notice unless your $fpath entries are numerous and deep
> The tradeoff is that the third one occupies less memory than either of the other two (though about the same as the alias) which is significant if there are a lot of seldom-used functions.
I expect that I have more $fpath entries than usual, but the total number of autoloadable functions is much more.