I think that defining 'it' too strictly is causing some confusion. The word 'it' has a whole range of functions, including to refer to facts, events, or situations. In the explanation you linked, the author claims that the sentence
Joe needs to prepare a list of all the projects assigned this year and to do it he needs to meet all the teachers.
is incorrect because 'it' is replacing an action (not a noun). However, I'd be surprised if any native speaker would consider this unnatural or ungrammatical. I do agree with the point that only 'do it' should be used in the case of a noun ('the project'), but I think that do it/do so are interchangeable in the case of an action ('prepare the project').
I need to plan out the month's schedule, but to do it / do so I have to find out my work rota.