encoding's stated purpose is to handle scripts written in encodings other than iso-latin-1, but as explained already, it affects other things as well.

Due to other problems with the module (but possibly including this problem), use of encoding is seen as buggy by Perl's authors.

Script's encoding:

• If you wish to execute scripts encoded as UTF-8, use utf8. (e.g. use utf8;)
• Your only other option is really iso-latin-1, the default.

Output encoding:

• If you wish to output characters appropriate to your locale, use open. (e.g. use open qw( :std :locale );)
• If you wish to output binary data, use open. (e.g. use open qw( :std :bytes );)

Sounds like you need use open qw( :std :bytes );.
If your script is UTF-8 encoded, you'll need use utf8; as well.