Hi,
Interesting question. I hope that I understood you correctly.
In general, you will see the amount of product flow without a provider in the inventory of your product system. But this works for product flows on the input side. However, if it is in the output table, you will have a multi-out process that needs to be solved somehow. So, yes, there you will not see it because openLCA works with one reference flow and not two per process (product system). Also, "Another use case would be a waste-to-product process, where a waste treatment process has a waste input flow and a product flow output." -> delivers two functions (waste treatment and production of product XY) and hence requires allocation.
So in general, the disconnected flows are there. What you describe is an allocation issue as it is not possible to hold two reference flows as quantitative reference. All the LCA databases I am aware of solved the multi-output issues for you already and you only have one product flow as a reference.
Hope this helps