Turns out that I had a few issues - the first one being that my headers weren't actually being sent from my header method at all in mod_perl mode. However once that was fixed I found the following solution: 1) header takes a hashref of _correctly_ named headers i.e. instead of -type and -cookie it needs Content-Type and Set-Cookie and bake() isn't needed at all i.e.

$self->cgi->header(
        {
            'Content-Type' => ( $args{type} || 'text/xml' ),
            'Set-Cookie' => $self->cookie,
        }
    );
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Once that was changed my original calls to cgi->cookie didn't need any changes for mod_perl mode.