I grew to heavily dislike the idea of just executing random code to configure things. Impossible to expose to tools, even harder to reason about it. Note that these files do not contain python code at all. They just sometimes contain little Jinja templates.
The idea is indeed that the GUI can eventually edit some of these things. It also is already used for `lektor plugins add` for instance which updates the project ini file.
Lastly the reason ini over yaml is purely that this can preserve comments and doing the same for yaml is a lot more work i did not have time for :)