First I'll repost the "problem". Or what I have read is a "problem" by others.
In this example we have two thieves, Annabell and Lucy. One is a human rogue and the other is a half elf rogue.
Annabell has chosen her primes. Her primes are DEX, WIS, and INT. She has chosen to capitalize on her rogue abilities by choosing primes that are connected to all her rogue abilities.
Lucy on the other hand has chosen CHA as her second prime. She has chosen to be a grifter type. Able to fast talk her way out of trouble.
Now lets say neither of these rogues have attributes that give any bonuses. And both rogues got to pick a lock on a door. The door has a simple CL1 lock. Pretty simple lock to pick. Both rogues have Dex as prime so both would need to beat a 12 or higher to pick the lock. Since the CL1 cancels out level bonus the roll is just a straight forward 12 or higher. This is pretty simple.
Now lets say both rogues pass the door. Both rogues know that the lock was just too easy for what could be a great reward just beyond the door. So both rogues want to try to "find" traps. And of course the room is trapped. The craftsmanship of the trap is not the best, But it is no armature work either. So the CK assigned a CL of 4 to the trap.
So Annabell has Int as a prime. Her difficulty would start off as a 12 with the CL4 added on. For a final difficulty of 16. She adds her level to the roll.
Now poor Lucy on the other hand doesn't have Int as a prime. So her starting difficulty is 18. With a CL of 4 as well. So she has got to roll a natural 20 to detect the trap. Since her final difficulty is 22.
I myself look at this and it makes sense to me. Lucy chose to not have her Int as a prime so she is not good in any of her skills the are not Int based. I do not see this as a flaw in the rules but rather a level of customization.
After all I could choose a rogue with Str as my second prime to be a bit of a thug. Or Cha and be a confidence man and fast talker.
If the above example was turned around. And this was a social roll. And both rogues were trying to talk their way out of trouble and the it may very well have been Annabell needing the natural 20 and Lucy skating by with a low difficulty.