I’m confused – are you creating WebHelp or HTML Help (chm)?
I realize I didn't say this outright (sorry!) but it's HTML. I want to change the default window setting for RH to the appropriate window type for HTML (chm) output.
I think this is an easy change. Under Single Source Layouts, if you right-click "Microsoft HTML Help" and select Properties, there is a field on the screen called Default Window. Set this to "Main", and click "Save". When you generate the project going forward, it should use the Main window properties to generate the project, which I think is what you're looking for!
(I had to open my version of RH to look at the settings, and that's how I currently have it set up.)