Setting the SKIPCONFIGUREIIS property via an immediate CA (scheduled prior to 
ConfigureIIs of course) to simply skip IIS configuration when the target host 
already has the website installed would require us having some way to determine 
if the target host already has the website installed wouldn't it?

Yes


Is there some wix syntax supporting that check?

No, you would need to write a CA to query the IIS metabase.


Also wouldn't doing this actually cause not only our AppPool and WebSite 
settings from not being applied but also all of our iis:WebVirtualDir and 
iis:WebApplication settings that we do want to recreate every time as we do 
remove those components during uninstall.

I'm afraid so, as Rob pointed out, it's a nuke.


The addition of the ConfigureIfExists="no" option to our iis:WebSite element 
sounds promising since it sounds like it may prevent the activity that is 
traversing any of the child vdirs that someone may have added to the website, 
outside of what our installer creates, and resetting their appPool setting to 
whatever is defined for the iis:WebSite.

I wouldn't be so sure. It'll certainly bail out early and skip some 
configuration (AutoStart, ConnectionTimeout etc and perhaps a select set of 
child elements e.g. SSL certificates and HTTP headers) but all bets are off 
without poking about in the source first.

IMO, the behavior is not entirely unsurprising but is clearly undesirable for 
your requirements.

Perhaps an alternate approach to the aforementioned nuke, once the exact 
behaviour of the extension source has been understood, is to insert temporary 
rows into specific IIs tables via immediate CAs that are conditionalised on the 
state of the box i.e. the presence/absence of certain items. This should allow 
you to dynamically adjust the install/uninstall behaviour of your IIs 
configuration process.

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