And the CustomActions should handle that just fine.
I believe you can have multiple sites on the same port if you are using host headers to select the site.
X2 Systems Limited
From: firstname.lastname@example.org on
behalf of Rob Mensching
Sent: Mon 19/03/2007 17:16
To: Tina Basinger; Wix Group
Subject: Re: [WiX-users] ConfigureIIs skipping virtual directory
You can’t have two web sites running on the same port so the CustomAction doesn’t differentiate today.