From what I found so far you can't mate flexible sub assembles, however it seems to be odd.
Simple example:
I have a standard clamp with limits so I can adjust it to part at the final assembly. I want to use this clamp on any part that fits under the limits of the clamp.
At the finial assembly the clamps move as I want but now I want to mate them or somehow lock them to a part but I can't.
Not sure if I do something wrong or this perfect solution is not fully develop by SW?
I rarely use flexible sub-assemblies, but I'll try to help. You can mate them, but you can't mate one component of the sub-assembly to another one in the upper level assembly. You should be able to fully Mate it by mating to other components.