Disabling the embed unlisted setting will not prevent the RSS posts from appearing on the homepage. There are some details about how that setting works in the OP: https://meta.discourse.org/t/configure-the-discourse-rss-polling-plugin/156387#prevent-embedded-topics-from-being-unlisted-3. That setting is somewhat confusing because it was added to solve a problem that can occur when Discourse comments are used on an external site. The setting doesn’t make a lot of sense when used with the RSS plugin. That is why the OP suggests disabling it.
I think for your case the best solution will be to disable the embed unlisted setting and follow @Jonathan5’s advice of publishing the topics to a category that is muted by default.
If you publish the RSS posts to their own category, you can add that category to your digest suppress categories setting to prevent the topics from showing up in the digest emails.