But there should be an association between the instance of assembly1 and the two instances of subassembly2
My theory is that the structure is similar to Product Structure, though if so, the tables aren't named similarly. I've tried multiple variations unsuccessfully.
Otherwise you'd have to map it through the product structure and somehow have to align the instances to the instance of the where used. Which I believe is what PTC did for that table, which also explains how it is now failing for some of our use cases as you drill down further in the structure.
Any other query builder gurus who have solved this mystery? Is anyone else out there using Configurations and Instances?