Hello Michael Johnson and Mozzers,
I have seen Shopify do this a few times, though I do not have clients on that particular platform at the moment. It is frustrating. You're right to want to resolve this issue. Between duplicate content, authority conflicts, and an inflated crawl budget, one issue or another is bound to hold back site performance.
Is this what you would do? Not immediately, no. I want to see those pages canonicalized. That way, your preferred pages get all the juice back from their respective canonical link. Is this an option for you?
**Deindex request... and s_ide effects?**_ Canonical tags would make these part irrelevant (yay less work!). To be thorough though: I'd let Google figure it out unless you have strong evidence your crawl budget is maxed. And I don't see any negative side effects from noindexing duplicate content. If worse comes to worse, you have a good plan.
Shape that content,
CopyChrisSEO and the Vizergy Team