org-mode VS scimax

great article, I personally like that with ox-extra, you get the ability to put :ignore: and :noexport: tags on org-headings which allows you to have many many sub-headings, most recommend 2-3 headers (see Tufte and Butterick as to why), I personally find myself naturally making many sub-headings (topic, subtopic, minitopic, argument, counter-arguement, variation of argument, etc) with :ignore: those go away in export, and with :noexport: I can add miscellaneous and experimental stuff.

Scimax should have out of box setup for bibliography, references etc. Anyway, regardless of what you use Emacs for, one step a time, would be my recommendation. Just start using it and solve problems as you experience them. It is better to add a single thing at a time when you need it, than to add 1000 different things because you think you will need them, and then not know what you have or what causes a problem.

https://github.com/wdavew/org-excalidraw is close. I discovered you can install Excalidraw from Chrome, and then it is like a local program. That is pretty amazing in itself. org-excalidraw indeed offers an org-link and way to make an excalidraw file from emacs, edited natively in an external excalidraw window. The svg preview does not work though if you use freehand lines in your image, and I was unable to install the npm packages on my Mac for some uninteresting reason related to DNS, but it did work in a node docker image. I find writing in excalidraw less advanced than in tools like Notability or PDFExpert. There are some artifacts in excalidraw from smoothing, or dangling pixels that I don't love. I forgot I had previously used https://github.com/lepisma/org-krita. Krita is a full drawing program, and this integrates into org-mode with image previews nicely. I am not that skilled in using it, and as a full drawing program, it has a learning curve. I wrote https://github.com/jkitchin/scimax/blob/master/scimax-inkscape.el to integrate inkscape into org-mode. It works, but I find inkscape slow to open, and I am not that skilled in using it.

Maybe give scimax a go?

Anyway, if you want something geared toward scientific usage, there is Scimax by J. Kitchin. There may be some others, but I am not aware off.

Apart from the ones already mention, John Kitchin's science-focused Scimacs is also an option.