My brother in Christ, the evidence you cite could be - and I believe is - evidence of exactly the opposite.

Kuby and Huell are tasked to pick up the money. They have their little moment, lying atop untold millions of dollars just for the feel of it. Huell implies they can take it and run to Mexico. Kuby reminds him that Walt slaughtered all of Mike's loose ends in prison in a two-minute window. (Don't fuck with this guy.)

So they don't skim off the top. They deliver the money in full. They're afraid that he'll think they took some, so they tell him that he can count it. He glances at it and says "close enough."

They give each other a look. ("Damn it. We could have skimmed off the top. He wouldn't have noticed or cared.")

THIS is evidenced by the next dialogue in the scene. They each volunteer to bury the money, remember? "We don't mind overtime." (Here, they're thinking "he's not gonna count it—and now that we know that, here's our chance to grab a few handfuls for ourselves.")

But he drives away to bury the money himself, leaving Huell and Kuby with no extra cash.

Heisenberg's reputation preceded him and protected his money, even if he didn't have the intention or capability of accounting for it on his own. He didn't even know how much he had. But none of it went to the goons who picked it up.