I'm not sure it's bug, game limitation or intended feature, but I guess this worth reporting.
Reproduction: Make any craft in your designer. Make it two separated crafts with respective command pod. Put moving parts on both crafts and keybind them to whatever you want. Fly your craft. You can control both craft with the key.
This is my video exploiting that. The tower and the rocket/crawler are separated crafts but I can control both at same time. You can see what I said around 5:30.
@AndrewGarrison Ah okay, got it. Thanks!