This is a nice project and nice writing about problem when there seems impossible to drive fan with three wires using PWM and read RPM at the same time. The problem seems to be that driving fan with PWM signal gives same PWM signal on yellow wire instead of RPM. So Giorgos came to solution to extract RPM signal even when fan is controlled by PWM.
He simply tried to find you how the PWM signal distorts the RPM signal on a yellow wire and he saw a difference which helped to construct a simple circuit with 4049 buffer which gave nice and clean RPM signals that are fed to POC microcontroller. This way it became possible to have full and easy control of fan speed and have RPM readings for feedback. I really liked how this guy disclosed the problem and how he moved towards a solution.