Why is it that at maximum i can get only 29 flat armor pen but magic users can acquire up to 64 flat magic pen?
Because AD and AP are supposed to feel really different as build paths.
Life steal and Zhonya's illustrate this pretty well ATM.
With sustained damage-dealers wanting some defenses, you can get life sustain to sustain long enough to do sustained damage.
With AP burst casters wanting some defense, you get a burst of defense after you burst so your CDs can tick down and you can burst some more.
If you look at specific aims in itemization you'll also see a lot of patterns like this. If you want MS, you generally need to build attack speed, you don't usually get MS with raw AD. If you want life-steal you need raw AD and you can't get Crit or Armor pen with them.
Seperating stats like this, or at least their quantity in a certain build, really emphasizes what the build style does - it offers a certain play style, a solid choice, and some pros and cons to go with it.
If you could just get every stat you wanted in any particular build, rather than having champions that offered a solid and distinct range from red, blue, green, pink, and yellow - you'd just get a whole lot of boring poo brown.