Substack supplies an RSS feed for each site, but there is no information included within that would help discern whether a post is paid or public. Filters based on searches such as "Read more" create too many false positives and are unreliable. After playing with this for quite a while, I realized that if you scrape the site yourself you can create a flag for paid articles and have FreshRSS mark anything with the flag as read. It only works with FreshRSS version 1.25.0-dev or above, since there was previously an issue with flags being ignored during scrape operations. I've included example code for Many Such Cases, written by Magdalene J. Taylor. I highly recommend that you subscribe and follow her writing, as she is tremendous! All you should need to change is the title and URL. As a bonus, this scraper also supplies a larger thumbnail image than the official feed. Substack RSS feed (with filter for paid articles)
Here are the solutions I find on my own once customer support tells me they've exhausted all options.