“Question: What is the purpose of all the tickboxes for the loaded master flat/bias/darks and all the created files in the filelist?”
For images that are stated as processed, there is no function.
For all lights, bias, dark, flats, master calirbation frames and BPM, the boxes can be used to deselect images and remove them from the file list. If you deselect a master calibration frame, it wont be applied to your lights in a following process.
A deselected light won’t be used in a process from 2) to 6).