Thank you for clearly explaining the use case. You have a complex simulation, no doubt, and you may be correct that Match Control is only good on a single body.
In my experience, if you have multiple bodies that have frictional contact over many faces, it can be very beneficial to take those bodies into SpaceClaim and put each body into its own Component. Then at the top level assembly, planes or surfaces are created that intersect multiple bodies. In each component, Split Body is used with the assembly level planes and surfaces, then with just that Component open, use the Share button on the Workbench tab. Repeat this for all the Components. This process results in easy to mesh solids in each Component. Shared topology makes the mesh congruent within the body.
In Mechanical, there are now smaller faces that are much easier to apply simple Edge Sizing mesh controls that result in Components with faces that will have Frictional contact with another face having the same number of elements along the coincident edges.