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I am not too familiar with feeds so i may not be able to provide too much insight. I was just surprised to see them when testing the feed page.
If feeds are only grabbing excerpts, then the simplest thing would be to just strip away the whole shortcode. We would loose the content /effect resulting fom it, but retain the essential and get a clean text.
There may be cases where the shortcode provides important content, and were people may wish to be able to evaluate the shortcode and pass the result to the feed, but this is probably a can of worm as there will be many different cases. Like you may not want to pass the content of a youtube one but pass another... this is really your call based on complexity.
If there is an easy way to just strip all of it , I would start with that.
Thanks for listening