[Animats]

That's the sort of thing I had in mind. Low-level Arduino-type microcontroller programming on a bigger engine.

The Arduino development environment is just an IDE and a library for board-level systems. It's C++ underneath, and all of the C++ language, although not the libraries, is available to you. You can do the same thing without the Arduino system, but setting up the build environment tends to be complicated.

If you need precision timing, you either need to program bare-metal, or use some hard real time OS like VXworks or QNX. Here, where it's all stepping and reading encoders, bare metal is the way to go. If you were coordinating a multi-axis machine, a real-time OS might be better.