(My physics education is limited to some undergrad level classes, so sorry if my interpretation is erroneous)

Could it be that spooky action has underlying causes that we can't tell yet? For example, reusing the flag metaphor- you and your friend decide to MAYBE wave a flag every day at 1200 GST, and then in practice it happens that every sunny day you both wave it (because hey it's sunny, everybody likes to go outside) and on rainy days no one does (because it's warm and dry inside in your house).

An alien with no knowledge of meteorology and our reaction to it observing this would always observe that either both flags are waved, or both are not, in a seeming random matter, where in fact it is not random at all.