As has been pointed out, the idea is to get an idea across to a student, whether it be the correct attitude or a point of airmanship.
I totally agree that the position of the control wheel pole is irrelivant during take-off - it's about making the "picture" out the front right. You can use fingers, screws on the cowling, air vents (on Cessnas), compasses, or anything you like to get the idea across to the student. That's what counts. As pointed out, perceptions/perspectives vary from student to student. The shouldn't vary for a student every time s/he gets into the same aircraft.
The purpose of identifying the flaps lever prior to raising flaps in a fixed wing is to engrain in a students brain at an early stage that it important to do things conciously rather than automatically. Later, when the student moves on to an aircraft with a retractable gear, s/he will hopefully not raise the gear by mistake (as has happened so many times before, and will again). The validity of this is questionable, but the intention is to have the student think about his/her actions.
Centaurus - Just curious, are you an instructor?