I think I may have ran into a similar issue that you are having while testing a MatterMost install for our team. The issue with us is that in the .jsonl file, HipMost was interpreting the exported HipChat channel as a “direct_post”, which to MatterMost, is a direct message. This seems to happen with private rooms converted using HipMost from HipChat exports.
The fix was to change the .jsonl file and substitute the “direct_post” to just “post” and remove the “channel_members” object. This seems to be working our development setup. I implemented the fix outside of HipMost using a Python script, which I unfortunately am probably not able to share due to some legalese that I had signed prior to employment at my company. However, I suspect that such a substitution can be made into HipMost, by someone with the appropriate ruby programming experience, or just a straight bash script using sed.