Yes and no. This edition uses the Experience Bonus which is half the Intelligence characteristic. If you have earned an experience check, then you roll and add your Experience Bonus to the roll. If the roll exceeds your current skill level, then you increase the skill by 1d6 or 3 percentiles.
Under the Skill Improvement section, it doesn't provide an optional rule that utilizes the optional characteristic category modifiers rule. I think that this was probably just a mistake in not including this extension of the category modifier optional rule.
Personally, I will be using the Skill Category Modifiers. Therefore, the skill category modifier for a particular skill will be added to an experience roll.
Jason-
Was this omitted for space reasons, or simply overlooked in compiling the book?