I was able to fix this issue by adjusting the 'Get Records' object. Previously, I was just getting Quote Line Items, but I was NOT getting QuoteLineItems from the specific Quote Object, therefore the flow was always returning 'true'.
The doc on how quote sync works doesn't really get into the nuances much.
There's some different scenarios not explicitly called out that occur below:
If you create a Quote from an existing Opportunity with products already on the opportunity, the Quote Line Items will be created for the quote (although you still need to click "start sync" for it ...