Well, with the way perk tokens go top to bottom, I actually find that I can save up perk tokens so that on later levels, I automatically get the extra perks. So, I think the game might be filling those slots invisibly... so there might be more to it than simply changing it in that way.
You are correct, it does 'invisibly' fill up those slots. My suggestion attempts to provide more options for the earlier perk tokens. For example, if you are level 12 and have 6 perk tokens, the current system (4 per level) gives you (2^6)*(4^6) = 262,144 options. If you filled up 3 per level, then you would have 3^12 = 531,441 options. Please correct me if my math is wrong.
However, some people want their perk tokens available earlier (since there are 16 levels total, you would have to get MORE perk tokens to fill up the earlier perk levels), rather than have some unusable perk tokens in levels they may never actually get before beating the game. That is why I included the possibility of filling up the tokens to 4 slots for current levels, and then fill up 'normally' afterwards. I hope that makes sense...I have a small adrenaline rush from forcibly crashing AI war