Replying to my own question, but not an answer. If you add this config to web.xml:
<context-param> <param-name>facelets.SKIP_COMMENTS</param-name> <param-value>false</param-value> </context-param>
IE (only the versions specified by the conditional comments) just spits out the full a4j:loadScript tags, so that's not a solution. In other words, the conditional works, but the a4j parsing doesn't.