You should know that it's possible to write as low-level "from scratch" code as you like in the Arduino IDE. The Arduino platform does like to offer a more high-level, beginner friendly option but it's not absolutely forced on you.
For example, the IDE will automatically generate function prototypes in .ino files for you but if you don't want that you can either just add the prototypes yourself or put your code in files with other supported extensions (.cpp, .h, .c, .S, etc.), which the Arduino IDE doesn't do any special preprocessing on.