I understand the default Git behaviour of updating the modification time every time it changes a file, but there are times when I want to restore a file\'s original modifica
Git does not do this. Like your linked FAQ says, it would break using timestamp-based dependency analysis tools like make.
Think about what would happen if old time stamps were applied to files checked out from ‘old’ commits:
But, if you really want it, all the information is there. You could write your own tool to do it.
In your case, just use something like touch -r configure configure.ac to reset the modification time of only configure.ac, (or bring configure forward in time with touch configure).
Actually this is an easy “exercise for the reader” if you want to practice reading C code. The function that changes timestamps is utime or utimes. Search the code for uses of those functions (hint: git grep utime in a git.git clone). If there are some uses, analyze the code paths to find out when it updates timestamps.