Basically, the issue is that the current MP version, that you can download from HERE , raise an alert saying that the "MEX Endpoint Is Unreachable" even when it is fully OK.
The issue for this false positive seems to be that the script does not exclude from the check, those servers whose role is not "PrimaryComputer". Having that said, I created a modified version of the script (and of whatever is needed to run it) and put it into a simple addendum MP that contains the following:
A DataSource module which contains the fixes script used to perform the check only on PrimaryServer role
A UnitMonitorType which parses the output from the DataSource module
A UnitMonitor which contains the script body and reports on the MEX health by creating an alert in case the status is not good.
A pre-defined override to disable the original monitor.
This addendum MP, only works with the MP version released by Microsoft for Active Directory Federation Services 2012 R2. To use it, just import it. No need for additional overrides or configuration.
If you want to give it a try, download the Zip file from the link below and import it.
I hope this addendum will relieve your pain, a bit.