I think your instincts are correct. A 36-question form in a narrow modal popup window could create a number of challenges:
- What if the user accidentally clicks outside of the window and closes it?
- Lengthy scrolling in a modal window is a poor experience.
- What does this look like on mobile (if that's a consideration)?
Consistency is definitely one of the most important UX heuristics, but contemporary UX thought leadership advises to balance consistency with flexibility:
It’s natural that designers look for consistency and try to build
visual systems. However, when focusing on building a consistent
experience, it’s easy for the goals of an end user take a back seat
which ultimately compromises the experience we set out to improve.
Flexibility is often seen at odds with consistency, but for a design
system to scale efficiently and effectively both need to be balanced.
How they’re balanced depends on the personas and workflows for your
products.
You might need to convince your leadership that breaking with the design system is the right thing for the user. If they are not open to this at first, go ahead and implement the questionnaire in a modal and watch the abandonment rate. Suggest testing a full-page version in an A/B test and see if you get better results.