The double strike killed off the match as a competitive spectacle, although Jermaine Pennant flashed in a couple of long-range free-kicks to give Birmingham some hope.
Trott's 102 from 126 balls - astrike rate of 80 - contained six boundaries, compared with his unbeaten 84 in the previous match which featured only three fours and astrike rate of 70.
But with Herath gritting it out at the other end, McKenzie took charge, dominating the strike and hitting two sixes over square leg off Adams, before a third sealed the match.
Pompey started the match brightly and Ciftci's early strike - which came after he took a short corner from the right to Matt Ritchie before getting the ball back and beating Royals goalkeeper Adam Federici with a right-footed drive - was deserved.