I have read the darktable manual section about editing an image: scene-referred workflow and tried it and it works well for me and has given pleasing results. The manual seems to place great emphasis on the order that the modules are applied and whilst I don’t pretend to understand the technicalities of the chosen order of modules, I am surprised that cropping the image is not recommended as the first step. My reasoning for this is: Supposing you shot a scene using a prime lens and could not avoid including a very bright area of sky. You shoot the image with the intention of cropping it to remove the distracting area of sky. If you use the exposure module as a first step without any drawn or parametric mask, I presume that dt will take an average of the scene which includes the sky portion. If you then adjust the exposure using the histogram as a guide, it will result in the rest of the image being underexposed. Alternatively, if the image is cropped first, the histogram will reflect the true luminosity of the the image. I have been editing digital images for many years and always used the crop tool before anything else so I’m curious why this is not recommended with dt.
I always crop as the first step.
That is different from the order in which the modules are applied.
The crop module comes before the exposition in the pixel pipe.
So, I don’t think the problems you describe applies.
As Colin said, there is a difference between the order in which you modify the modules values and the order they are applied in the pixel pipeline.