Under full throttle take-offs the secondaries do help if I don't rev the motor to spool the turbo. Remember, my turbo doesn't spool till around 3000+ with full load. There really seems to be no penalty to having the secondaries remaining in the motor. If you look at the dyno sheet there is no underpowered sections, its pretty much flat across the top. Also, the way I ported out my secondary intake runners had long ago reduced the dip in power when they open up. THose benefits have just carried over with the turbo.
The best thing about the secondaries is saving fuel now. If I'm cruising around town and they keep the torque high enough for the car to act normal.
Former owner of '99 CSVT - Silver #222/2760
356/334 wHP/TQ at 10psi on pump gas!
See My Mods
'05 Volvo S40 Turbo 5 AWD with 6spd, Passion Red
'06 Mazda5 Touring, 5spd,MTX, Black