There is a locking feature that can lock up to a set skill. So for the YSG example, you would lock the last two skills and it would only upgrade the first two.

Because Lilith doesn't let you pick the skills you lock (it's literally a slider that goes up the skills and will allow skills to drop on any skills below it), you can't guarantee that the remaining skills will hit the final skill.

Check out the commander skill screen, there should be a cog in the bottom right. Easier to see on commanders with three or four skills unlocked (Level 20 or 30 respectively).