Hiding bones during construction is not properly displayed by level instances placed at editor time.
Note that setting 'Update animation in editor' on the mesh and re-running the constructor script(by dragging) can make a level instance properly hide the bone. However this can be an undesirable workflow and it seems that on PIE, these instances will revert to showing the bone again.
Place a BP with a skeletal mesh component in the level.
In the BP's constructor, hide one of the skeletal mesh's bones.
Result: The BP's viewport hides the bone. Instances in the level do not hide the bone. Instances spawned during PIE hide the bone.
Expected: All instances should hide the bone.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-83102 in the post.