Interesting. Given how it's required to specify which custom type relationships exist I can understand why this is the default but it's weird that you don't have the option to change it.
Based on @samlittlefair's comment on your post it sounds like it should be editable from within prismic slicemachine, but even on the beta branch (which I'm using currently) there's no option to allow document relations even with custom type options
I wonder what the 'correct' solution is here? Random document links won't work unless you define every document relationship in the initial query (very inefficient), so just deleting the web type here doesn't really work as a solution.
I guess a perfect solution would be for the linkable documents to be selected, which then automatically adds queries to your fetchLinks property but that's definitely not how this works now.