The first employee is getting this percentage before most of the dilution, whereas the CEO is getting his grant after some dilution has happened. So you can't compare E#1's 1-2% to the second CEO's 5%, because these numbers are at different stages of the dilution process. (Generally, you don't have a second CEO before a few rounds of funding have occurred.)
Also, the first employee may not be more important than your second CEO, but he should certainly not be outranked by post-funding VPs.
How true is this really? Employee #1 is getting diluted way down if the company takes a B round, but isn't getting diluted at all if the company gets snatched up early.
Should your first employee be outranked by a post-funding exec? Well, Twitter hired Dick Costolo. You need some pretty amazing Django chops to "outrank" him.
Also, the first employee may not be more important than your second CEO, but he should certainly not be outranked by post-funding VPs.