fix: fix replace with array dependent parameters

[AayushSabharwal]

Close #2932

Checklist

• Appropriate tests were added
• Any code changes were done in a way that does not break public API
• All documentation related to code changes were updated
• The new code follows the
  contributor guidelines, in particular the SciML Style Guide and
  COLPRAC.
• Any new documentation only uses public API

Additional context

Add any other context about the problem here.

[AayushSabharwal]

I haven't added a test because I'm working on removing parameter dependency handling from MTKParameters altogether, and moving it to codegen.