If I read the article correctly the upgrade mechanism was vulnerable but that is no longer the case with the recent builds.
That's correct. It was fixed in MBAE 1.04. So unless you have 1.03 you are not vulnerable. Current version is 1.05.
"The upgrade mechanism in OLDER versions of Malwarebytes Anti-Malware and Malwarebytes Anti-Exploit" People now do not read more than one line of text , and it was on the first line!
While I can't speak for Malwarebytes Anti-Exploit or MBAE, Malwarebytes Anti-Malware has an internal update mechanism that prevents older versions from being maintained and run. The current MBAM software is not vulnerable to MitM or Man-in-the-middle attack attacks.