The difference between ISM created by Actor/Merge/Batch menu and those by Blueprint/Houdini is whether the Instance Hit Proxy is generated.
I add NewISMC->bHasPerInstanceHitProxies = true; in HoudiniEngineBakeUtils.cpp before OutBakeStats.NotifyObjectsCreated(InISMC->GetClass()->GetName(), 1); and now ISM actors baked by HDA works the same as Acto/Merge/Batch.
I never try it in blueprint but the idea is to turn on the flag to generate instance hit proxy.
Hope this helps.