I don't know what those scripts are, so please give links. I would need to see the script.
Z Systems is the name of a series of scripts, but it sounds like you are referring to:
Alternate MP X?
Anyway, I don't know if there is a solution in the abstract for other scripts not drawing the alternate MP. As it is, the script overwrites the Window_Base method, so that is a good step, but there is no standard method for drawing mp on sprites, so any script which is drawing MP on sprites would have to write a new method specifically to do that. It would be impossible for Zetu or any other scripter to anticipate and accomodate for every script that might be written in the future. The offending scripts need to be identified, and then a compatibility patch can be written.
Anyway, I'm not really sure how that is supposed to interact with your request. Do you not just want to show the Enemy's HP with a bar but also its various forms of MP?