Intel provides an IoT version of their sdk for C/C++. I can say that none of my development is via Arduino.
I have the mini break outboard, Linux booted, ssh into console and develop in Kylix3 (pascal) or gcc C/C++ (onboard), so I can choose to use or not use the IDE.
Python is also onboard.
Pin programming is available via libmraa.
arduino sketches can be removed located at /sketch/sketch.elf and the loader can also be disabled using systemctl.
Your options are flexible, and you can use sketches, packages and your own Linux programming in any combination you see fit.