Judging by the security errors in the console about scripts not running, I would guess that some script that's supposed to unhide stuff isn't working. In this case, I think the issue with the mht file isn't anything to do with the MIME encoding of it like the last one and is an HTML issue in the HTML part. Look into it more later.
All scripts in mhtml files are blocked now in Chrome. See https://bugs.chromium.org/p/chromium/issues/detail?id=452901. So, the reason things aren't working right in the last mht file is because scripts aren't loading. There doesn't seem to be a way to disable the blocking. Scripts work for unMHT in Firefox though and when it saves things (when you use "current state" at least), it's displaying things as shown I think.
The only way to work around it in Chrome I think is to somehow modify the Chrome source HTML that loads the mht content in a sandboxed iframe where you use "allow-scripts" in the sandbox attribute.