The data for armor and penetration values were derived (with permission) from Panzer War. I believe Panzer War was published as a computer simulation later on.
Two page tanks was my initial foray into this realm and has it’s issues. Just the same it has a following. I don’t play Two Page Tanks anymore — admittedly it has its problems.
WWII project is geared along similar lines but uses 2D6 rolls which allow for a more detailed look at things.
As for your issues with penetration, all I can say is it depends on what you hit, where you hit it, the angle you are firing from and the thickness of the armor. All these criteria are virtually impossible to address in a game where you roll a single D6 (Two Page Tanks) or 2D6 (WWII project) for damage. One has to simplify and accept some potential inconsistencies if you want to avoid wading through a bunch of tables.
The WWII project was devised to play a very low level small unit game in 4 hours or less — hopefully with more meat on it than your ability to roll 6’s. That is the “box” that drives all else. Many fine ideas have been submitted for this game and ultimately rejected because the time needed for implementation was not justified by the benefit conferred.
All things considered WWII project is rounding into shape nicely. It does a nice job of modeling WWII combat and games (each player running a platoon) often run about 3 hours. The problem with WWII project is that players generally want to control a company — and this can run into some serious time (which is fine if you want to spend all day playing a game.
I have written rules that exceed 120 pages (Watch Your Six!). Perhaps the most comprehensive “game” (certainly not a simulation) dealing with Great War Aviation. Games often run 3-6 hours depending on the numbers of aircraft involved.
At the other extreme — Two page tanks is about as simple as it gets. All the rules appear on one page (both sides) and you need an additional page with the unit data. Scale is 1 turn – 1 minute.
Different strokes for different folks.