It's intended mechanic, you can cheat it by prestige right before 2nd or any byte amount, first 100%= you get 1 byte, without performing prestige go for next run and prestige at 90-99% area, then you will have 1 usable byte and will be able to earn another one pretty soon by reaching last % to prestige.
I wanted to make prestige system like that to try support all kinds of variations of gameplays. You could get multiple bytes per single run next prestige requirement is higher than if you had performed prestige at first it might not seem so,be noticeable at first but when have more than 16 bytes things start to take effects. These values are not final and is what I am working on.
This is how I tried to balance this kind of prestige system adding proportional negative to positive of earning multiple bytes in single run.
There are couple of mechanics I haven't explained yet, will try to do so in following days/next update, some things are just intented for player to find.