Is there somebody here using Nix(OS) who could teach me how to call this using a Python virtualenv where I deliberately setup pandas + seaborn before (in a shell)?

Well, I already wrote that this is not the brainstorming process but the next step: ordering items.

With my Emacs Org-mode:

- a
- b
  - c
    - d
  - e
- f

… mark everything and invoke C-c * I get:

* a
* b
** c
*** d
** e
* f

I don’t know what doom makes differently here.

I don’t know about your brainstorming process.

When I do brainstorming, I don’t arrange the items in the initial phase. Instead, I create a list item, write my idea, press C-RET for the next item, write down the idea and so forth.

This results in an unordered list of ideas.

Only after finishing this brainstorming phase, I start moving items around.

Therefore, I don’t get distracted by order, commands, styling, arrangement, priorities, … in the brainstorming phase.

After I’ve ordered the items, I may convert the simple list to headings using C-u C-* (AFAIR).

HTH