I fixed this problem by adding the content ID to the cache file name. This nicely preserves the caching.
The attached patch below contains this fix for 4.0.0RC1. Additionally, the cache directory has been changed to cache/com_comment/feeds, in line with the Joomla directory layout.
Patch notes:
1. Apply the patch to /administrator/components/com_comment/plugin/com_content/josc_com_content.class.php
2. You have to manually create the directory cache/com_comment/feeds
3. As the patch generates 1 cache file for each article, you can end up with a lot of files in the cache directory.
My hope is that this could be incorporated into the next release
feed_cache.txt