It seems to me that the regular expressions used in the module's "regexp" and "insertafter"/"insertbefore" parameters could mess it all up in case the config files contain comments with the used strings, e.g. "# Following won't work without SSLEngine enabled".
Perhaps use the beginning-of-line anchor, e.g. "^[ \t]SSLEngine on[ \t]".
The trailing whitespace can be problematic as well - what if I have a line " SSLEngine on", that is, no whitespace after "on" ?