The modules compiled for the CPU (Linux side) are listed here: https://github.com/PX4/Firmware/blob/master/boards/atlflight/eagle/default.cmake
The modules compiled for the DSP (Qurt side) are listed here: https://github.com/PX4/Firmware/blob/master/boards/atlflight/eagle/qurt-default.cmake
mainapp.conf is the startup script for the CPU side, px4.config is the startup script for the DSP side.
Correct. Some modules can run on either side but others can't. For instance I remember that modules which need file system access need to be on the Linux side, however, drivers that communicate to SPI, I2C, and probably UART can only do so from the Qurt side.
We mostly tried to have as much as possible on the DSP side to free the CPU of resources, however, as said some modules couldn't easily be ported to the DSP and do not need the real time constraints like the estimator or attitude control modules.