Since there's as much replicated matter as original matter, it's a 100% increase in mass. That goes however it's spread out between them.
I'll illustrate with example numbers.
Original Kirk = 80kg (say).
Good Kirk = 40kg matter + 40kg replicated matter
Evil Kirk = 40kg matter + 40kg replicated matter
That's 80kg matter plus 80kg replicated matter, for a total of 160kg.
There is as much replicated matter (80kg) added to the original Kirk as he originally had matter (80kg), so it's a 100% increase. 80kg = 100% times 80kg.