The difference is that you are not doing inplace editing.

UPDATE

I now tried your examples. And partly I have different results:

Same result like you.

$ perl -e" binmode STDOUT; $|=1; print qq[\x0d\x0a]; " | od -tx1
0000000 0d 0a
0000002
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Different result.

$ perl -e" binmode STDOUT; $|=1; print qq[\x0d\x0a]; " | perl -e" use 
+open qw/ IN :crlf OUT :raw /; print join q/ /, unpack q/H*/, scalar<>
+; "
0d0a
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Here my perl version.

$ perl -v
This is perl 5, version 14, subversion 2 (v5.14.2) built for i686-linu
+x-gnu-thread-multi-64int
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