Both versions works correctly if HISMC is pre-placed (generated in ConstructionScript). Only when generated dynamically does it fails. The Navmesh isn't being updated after SetStaticMesh and AddInstance are called on the second blueprint. If you play in Simulate and move the second blueprint the navmesh will regenerate properly.
There is different behavior being executed between setting the mesh on the HISM component through the Detail panel compared to using the SetStaticMesh function on the event Graph.
This was reported and tested in 4.23.1 (CL-9631420). This was reproduced in 4.24.3 (CL-11590370), 4.25 Preview 1 (CL-11723679), and 4.26 (CL-11929415).
Results: One blueprint (with mesh set in editor) will generate navmesh. Other (with mesh set programmatically) won't.
Expected: Both blueprints should generate navmesh
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-90233 in the post.