First, sub-skills are those one that can be used by itself, I'll use the 'spell mastery' as example, you can't use it because is a sub-skill of spells, so without spells is useless.
The, why remove the limit?, the simple explanation is allow to use it from first level, if not, we can't use it really until medium-high level, but then we have the high level version of spells...an example:
Imagine a cleric that wants to specialize in blessing, usually he wants to increase the spell effects, for example cast bless I in 2 targets (1 extra target), increase the bless I R radius (so more people is blessed), etc.
For this, he usually need to wait until medium level (10-15) for having enough skill bonus (with 1-4 ranks is really impossible to use this skill, and is dangerous), but then, he can begin to use the skill when he has the bless III version, losing the interesting opportunity to do it with the I and II version of spell.
Then, removing this limit this character could use the TPs ranks in this skill, and surely in level 2 he could use DPs to have almost 10 ranks in the skill, so he could attemp to use it soon.
Now, is GMs work define the cost, but I recommend to use the first cost (if 4/10 then 4) for the initial 20 ranks (enough skill bonus to try to use effects as extra target with -50), and then use the second cost until the character gets level 20, so then we can use the real cost normally.
You can define your own 'sub-skills' to use this.