Thanks! Yes, one of the major design motivations wasn't so much to make a phone, but to make a nicely packaged device hackers can use at the hardware level for other purposes (we are practically locked out of modern phones for a variety of reasons).
Apps: The end goal is to embed a Python interpreter in the firmware, and then it would be a matter of interacting with an API in Python. Right now it's C++.
I'm not sure what you mean by "connect an API for a smartphone to an Arduino". Do you mean: What does the plumbing look like between the code that calls the API and some physical pin?