GURPS Powers 96 mentions:
- Take Affliction (p. 39) with Negated Advantage to remove specific advantages regardless of their origin.
The "regardless" makes it sound like variant versions can be target, and that "specific" refers to name and not modifiers, UNLESS you understand the distinction of terminology:
Based on points however indicates that specific may refer to modifiers, since it is designed to make it more versatile in targeting diffently modified abilities, as a cheaper alternative to Variable Enhancement: instead of being able to change to any enhancement (including any form of Negated Advantage) it only allows changing to a different arrangement of Negated Advantage which also targets a modified version of the specified ability.