The actor Blueprint is intentionally causing an object slice to occur. In other words, we're copying a derived type to a base type, so the expectation is that only the inherited base properties are copied from the derived type.
In this case, that doesn't happen at all. SetStructurePropertyByName seems to be a bit aggressive with checking that UScriptStructs match. Checking that they're from the same hierarchy should be sufficient, but we'll need to validate.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-207416 in the post.