Well done Leon!
I'm wondering if we should disable that cache store when running on CLI: while I agree on your second option - the issue is on cache invalidation and not on setting the value into the DB: set_config() does it on DB to persist the value and the invalidated the related cache definition... which is the CLI definition and not the WWW definition i.e. stale data on those WWW definitions running on ACP cache store "changed" by both WWW and CLI processes - , I wonder if there are other cache definitions which could create strange/dangerous issues like this one i.e. why not excluding that store when running on CLI (which requires some mocking or a check on PHPUNIT_TEST too for the tests purposes, I guess)?
HTH,
Matteo