The OS has permissions on the directories and if they don't permit a user to create anything in
/etc it would be a security hole if some other mechanism would have the OS open other files than it thinks it is doing. (If the user has the permissions there is no need to fool the OS, then she can just change the files).
That permissions on
/etc are normally as restrictive as they are is necessary in order e.g. not to have a user change provide alternative private keys for
sshd (by "fooling" the os not to use the ones from
/etc/ssh, and other system information for which integrity is important.
You can mount other filesystems over
/etc, and some of those can be handled in userspace, and thus possible by normal users without the OS noticing (in being notified of the change). But you still need root access to do the intial mount, so I would hardly call that fooling the OS.
You indicate that you solved this at your program and that is the level at which you can do the fooling, but of course that won't affect the OS.