This is because the RebuildControlMappings function only checks this flag when you have a mapping that was already added, we should apply this for any new mappings as well.
I'll update the repro steps with an easy case in L.yra while working on the fix
if I have a digital input action that maps to a key, if I hold the key down BEFORE adding any input context that uses said key, once the input context is added, all input actions involving said key will immediately trigger, even if I have bIgnoreAllPressedKeysUntilRelease set to true in the options parameter
Expected Result: The event does not trigger until you release M, and press it again.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-156910 in the post.