`setup.cfg` + `pip-compile` > `requirements.txt` = Dependabot buggy PRs

I encountered an issue in a private repository. I observed that this problem happens when the requirements are specified in a package's `setup.cfg` and then compiled into `requirements.txt`.

I have been able to isolate the issue in this repository: https://github.com/titouanc/demo-incompatible-dependabot-upgrades

_Originally posted by @titouanc in https://github.com/dependabot/dependabot-core/issues/3041#issuecomment-925157845_

Start by reproducing the reported behavior in the linked demo repository, focusing on dependencies declared in setup.cfg and compiled into requirements.txt. Then trace the Dependabot path that interprets those files and compare the generated pull requests with the expected upgrades. Done means the incompatible or buggy Dependabot PRs are reproduced and the affected behavior is corrected, with regression coverage where the existing code supports it.

Written by the indexing model from the issue text.