I found one to hack what you want: when you set the permalink as an existing page, then it will not be generated (the original page will be there), but it will still be available as a / page message in Jekyll.
So, if you had an index page for a portfolio with the following URL: /portfolio/index.html , and then in your /_posts/ you would have entries that would have this in the front YAML case: permalink: /portfolio/index.html , then these pages will not be generated.
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