It is my understanding that UPDM includes SysML and adds to it. If a System is also a Block under the hood, then I think ParaMagic should work for it, irrespective of further applied stereotypes. As long as the key elements with the right stereotypes required for ParaMagic are in place, then it should work. If you have any specific problems getting it to work for you, let me know!
Looks like when you set up a new UPDM project, you'll need to select the SysML option, which makes it so that System extends <<block> instead of just extending <<Class>>
I was able to get ParaMagic working with UPDM systems by removing the <<System>> stereotype, then adding the <<Block>> stereotype and re-adding the <<System>> stereotype.
It's also important to make sure that element properties are actually Value Properties and not just general Properties, or else they won't work ParaMagic tries to perform calculations.