Did the btool output look the same as what your expecting to see?
My comment about the bundle was that you've exported /opt/splunk/etc directly. Nothing in the docs said to do that, it should work as the indexer should still be able to figure out where the app artifacts are. I don't 100% know if it picks up anything else that it shouldn't be seeing. My mounts consist of apps/pooling/system and users dirs only nothing else (but that is shared storage not the search heads etc dir).
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