Is there a way I can tell my code to use the hard paths ... exclusively?
If I understand correctly, you want to do a "typical" chdir (as a typical user) to put yourself into a directory via a symlinked path, and then be able to use a consistent path string from this point, even while invoking a sudo process.
Try something like this maybe:
my $startup_path = getcwd;
my $symlink_path = "some/symlink/path";
my $working_path = getcwd;
printf( "Started in %s, chdir'd to %s, now in %s\n",
$startup_path, $symlink_path, $working_path );
I think it should be the case that the value of "$working_path" should always be the absolute, physical path, without any symlink component in it.