The Wix WebSite action has to be specified outside of a Component if you want to safely use the Default Web Site (by safely I mean the installer won't remove the default site on uninstall).
<Fragment>
<iis:WebSite Id="DefaultWebSite" Description="Default Web Site" Directory="INSTALLDIR">
<iis:WebAddress Id="AllUnassigned" Port="80" />
</iis:WebSite>
</Fragment>
My installer has a bunch of Features, and some are only enabled when IIS is installed. Disabling the features based on Conditions works fine, and no virtual directories or sites are created, but during install MSI still tries to contact IIS due to the WebSite action and fails on a machine without IIS installed:
"Cannot connect to Internet Information Server. (-2137221164 )"
I found something about SKIPCONFIGUREIIS but this doesn't seem to work in Wix 3.