Mate them into position in the assembly so they fit together as you want. Then when you go to run your simulation you use a bonded contact. This will then act as though the connecting faces are truly bonded together as you want.
Unfortunately with two parts, mating is probably the only way you can get them to actually fit together. Mating both of them until they're fully defined is the best way to do that, and that'd be possible through mating their individual planes together. The simulation will still work this way, although I realise it isn't what you wanted
Doing it as one part is probably the way you're looking for, and it is actually possible to do it the way you want to, you'd just have to do two operations (Boss-Extrude) instead of one. If the base of the centre also needs to be 0.05mm higher, you can set "offset" in the "from" section of second extrude
Hope that actually helps, I can't open your Assembly because I'm currently running 2016, but it also seems that you didn't include the parts which the assembly references either