Although the Boeing CST-100 Starliner and the Orion MPCV are designed for different missions (LEO vs beyond LEO), one might imagine a mission which could be served by either vehicle. Presumably, both will be equipped with the same type of docking adapter, but can either be mated to and launched on the same booster type? Do they have compatible physical/electrical mountings/interconnections? Or do the different mission types and therefore booster requirements preclude the need for any such standardization?
Short principle-based answer: Yes
They both use a Low Impact Docking System, so what one could dock with the other could too. For that matter, they could dock with eachother.
Here's the principle based part; Ever tried to hook up an old monitor to a new computer? Maybe you have DVI cable for your TV but an HDMI cable on your cable box? Adapters are cheap and easy to come by for these consumer grade items.
Same goes for your rocket. Granted, you probably can't buy an Atlas-to-Orion adapter online, but space agencies employ lots of bright and talented people. Engineers exist to solve these problems.
Also, vehicle assembly isn't as simple as screwing your payload into a launcher. You're not so much loading it onto a launch vehicle as you are building it into the launch vehicle. Again, your engineers are going to earn their keep - it's part of their job to make sure all the electronics and power hookups are linked together properly.