I know that mkp files are merely meant to create transportable/installable CheckMk extensions. Only those parts are delivered to the agent that are specified in the bakery plugin. (Note: I did not know this when I originally asked my question – there is a second thread that greatly improved my understanding: How to write agent rules?) Nevertheless I consider mkp files the clean way to write CheckMk extensions. If I can deliver something as a self-contained mkp file it behaves just like any builtin check. If I would opt for agent custom files two steps in CheckMk were necessary to make my agent plugin work: (1) enable it and (2) specify the needed custom files. A full-featured extension (that can be delivered as mkp file) only needs the first step.
Coming to your question: I have an agent plugin that needs to call an additional binary that in turn also needs to be deployed to the target system.
I could solve this problem using the previously mentioned bakery API documentation. Independently also Jiuka tried it out and documented the solution in my other thread (same link as above)