The way I read it is;
When you select a skill with a mandatory sub-skill, you choose one sub-skill. Any use of another sub-skill under the sub-skill outside the one you chose is at the penalty listed in the skill description (-20 seems to be common).
IF you want to, you can choose to buy the skill again, choosing another sub-skill. Now, TWO sub-skills are at no penalty, while the rest are.
There are also talents that let you overcome sub-skill penalties if you want all sub-skills you have to operate at the same ranks as your first sub-skill.
It's not two different rules. When you select a skill, you designate a primary. If you select the skill twice, you choose two primaries. The "non-primary penalty" applies to any sub-skill you have not chosen as primary (when you bought the skill).