At the moment opac-showmarc.pl directly renders XSLT, which breaks themes and is generally pernicious. It should use C4::XSLT and not break themes.
I don't understand the issue from the description. Multiple changes on the file since 2012, including use of C4:XSLT and something template related: http://git.koha-community.org/gitweb/?p=koha.git;a=history;f=opac/opac-showmarc.pl;h=232eac50a8578434fe76c2c77a82a34d6d2f66ed;hb=5a63c5baa23c5f8b1fdd343995f360147f519d4b I assume fixed.