Gengis, thanks for bringing this subject up!
I'm currently instructing ab initio integrated ATPL students and I even make a big point of some of these points when signing off solo students for solo flights.
If I don't like the way some items are presented when we check they carry out everything that's needed for their flight (charts, pen/marker , spare specs, etc) I ask them how is it gonna work in flight when they need it.
I am surprised and somehow disappointed how many times the students answer "didn't think of it that way" + "nobody told me before".
I also get a good feeling when a student presents a tidy navigation exercise and everything is organized.
Relieved to see I'm not the only "cockpit management bigot"