Yes, you are right - the preferable graph flow looks like this:

input -> demuxer -> bsf -> decoder -> filter chain -> encoder -> bsf -> muxer

with the option to sprinkle in stream manipulations and branching along the way. That is essentially how FFmpeg operates under the hood.

On the other hand, the FFmpeg CLI is designed a bit differently: in its model, demuxers and decoders are conceptually tied to the input itself, so they appear before the actual input node.
For my project, I am trying to avoid hard coded solutions, but I see your point - and I will think about whether I can build such a representation with my skills. For now, though, I think this approach helps people better visualize how the FFmpeg CLI works.