Getopt::Long lets you provide a reference to a hash as its first parameter, so that instead of this:
GetOptions('verbose' => \$opts{'verbose'},
'filemode:s' => \$opts{'filemode'},
'dirmode:s' => \$opts{'dirmode'})
You can do this:
GetOptions( \%opts, 'verbose', 'filemode:s', 'dirmode:s' );
I suppose different people may have different preferences, but the short form seems very appealing to me.
Setting modes on directories vs. data files is sometimes a pain in unix, especially if you're doing something like "enable group write access" on a directory tree and its files, and the files are all data (not executables): if you're using numeric mode flags, you have to do two passes, so that directories will be "executable" (i.e. searchable) while data files will not. So, it would be nice if is really nice that the script could just take care of this distinction and do both types in one pass -- or but it might also be nice to allow the use of symbolic mode flags, like "g+w", so that this isn't an issue.
(Updated after I fully understood what the OP's code was doing -- nice work.)