For anyone having this issue:
I had an open support case for a related tracking issue and passed it along there where it was confirmed as in my initial post that changes made to support the facebook conversion api for all events (not just purchase) had introduced the bug. Support believed it had been fixed and when I checked again in FB the error had resolved.
However, yesterday I saw it re-surfaced again and I brought this to attention of the support rep.
If you are still having this issue please file a support ticket with Shopify, take a screenshot of the error in your facebook event manager and say you are seeing duplicated event ids. You will not get support by posting in this forum thread. A platform like Shopify has 100s if not 1000s of open bugs to triage and prioritize. My background is in software engineering at large tech companies, if you want a bug prioritized then you need to get it reported, if enough customers report you can rest assured it will be placed in front of a developer to fix. That is the solution to this type of problem, no app or configuration on your side will fix it. The conversion api events are sent from Shopify's servers.