I'm sorry but I feel I can't explain it better than those links I gave you.

Whenever you experience that some things in Windows would be easier if done in another way keep in mind that MS is very reluctant to change things since that would break more or less every existing application out there. I.e. some things have a long history dating as far back as to Windows 1.0 http://en.wikipedia.org/wiki/Windows_1.0

You also asked why all these mapping settings exists when the screen is in pixels and that's because most things in real life isn't measured in pixels... These mapping functions make it easier for instance a CAD software to present a proper scaled drawing regardless if on the screen or on a printer. The physical size of a pixel on screen is huge compared to the one on a laser printer so printing using pixels will produce something completely useless.

Keep experimenting and you will probably end up realizing that most functions are not as stupid as you though when using them for the first time. They are there to assist you regardless of what kind of application you write by making drawing details a bit more abstract.