Parsoid doesn't support stateful extensions / parser functions at this time. In this case, it looks like your extension relies on state that has been setup earlier in the page.

Parsoid calls into the mediawiki API to expand parser functions and templates, and there is no page state available at that time. That is why the #arrayprint call inside the template works as expected (because PHP parser sees the array setup and that state is accessible to the following #arrayprint function). But, the second #arrayprint in the page doesn't have access to page state since it is a fresh call into the API.

The existing stateful extensions (like Cite) are supported by having native implementations inside Parsoid (as special cases that are used very widely). LST is another one that will be implemented.

We do have plans for native Parsoid extensions and being able to register them. But, we haven't implemented that yet.

The lack of the registration mechanism is causing us a huge amount of problems, particularly with SemanticMediaWIki and the array extension. It essentially means that Parsoid produces messed up output for us, which means we can't use it effectively.