Is there any way you can avoid that environment variable being set and only use binmode?

Yes, sure, it's just that it's distribution of App::* variety, end-user targeted, like "no serviceable parts inside", etc. Of course I can fix it (and should notify the author). Thanks for reminding about crlf being "alternative buffering" and therefore operating on raw bytes:

open my $fh, '>', 'tmp.txt';
binmode $fh, ':encoding(UTF16)';
print $fh qq(\N{U+010A}\n);
close $fh;
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output is invalid on Windows (fe ff 01 0d 0a 00 0d 0a). Should have used ':raw:encoding(UTF16)'. Oh, as I see prepending ':raw' regardless is a good practice since long ago, should have paid closer attention to such details.