How does mutation work?

The manual explains the mutation UI pretty well, but does a really bad job of explaining the mechanics. Here's what I've figured out so far:

• Clicking "mutate" consumes a mutation point and randomly generates two possible mutations.
• Choosing a mutation "locks it in" and further mutations become modifications to that
• Click "mutate" again instead re-rolls
• You can repeat the above until you run out of points
• At any point, you can click "apply" to apply the selected mutation or "cancel" to back out without doing anything, but in either case all the points you spent are gone forever

The bit that's confusing me is how bonuses and penalties are generated. The first time you click Mutate, you tend to get mutations with nothing but small bonuses, or with medium penalties but very large bonuses. If you select one of those, the following mutations have much smaller and more balanced effects, basically letting you "tune" the first one -- so you might select +4 Claws/+4 Speed, and then refine that into +6 Claws/+2 Speed by repeatedly picking +1 Claws/-1 Speed sub-mutations.

What I can't figure out is what counts as a "first time". If you just roll the first mutation (call it the "bonus mutation"), accept it as is, and then go back into the mutation screen and keep rolling, you get nothing but tuning mutations. But if you leave it alone and play for a while, your next mutation will be a bonus mutation instead.

So, what determines the occurrence of bonus mutations? Is it every ten points collected, or enemies killed? Every 20 minutes played? Or is it something more subtle, like every mutation point you collect giving a slight one-time positive bias to the RNG?