@kneops
My two cents:
Darktable pipelines work from bottom to top. As soon as I started to work as 
intended, it made sense to me. Collecting my favorite modules in my own group 
helps to speed up my work.
As you already realized, the modules can be reordered. The pipeline changes 
accordingly. This gives great freedom to users, but can mess up the processing, 
unforeseen effects can happen.
The user interface to reorder the pipeline is the same as you would like to 
have for apparent reordering (I suppose you would like to work from to to 
bottom). So there you have it: How would one distinguish between reordered 
pipeline and reordered module names?
The developers choosed "from bottom to top" and choosed to let users reorder 
the pipeline, which in my opinion is a good decision. I needed some time to get 
used to it, but I see it as investment to apply this wonderful and highly 
versatile tool in my workflow.
Hope that darktable turns out the same for you.
Urs
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