I use the internal GAIN controlers for setting the 100 IRE white point; gamma and grayscale are done via my Lumagen Radiance. That does function very well.
But I asked a good friend of mine who owns a RS40 too. He calibrated his RS40 like the way I told you before. And no, there was no problem with the RGB balance vs. gamma: you can adjust the RGB balance with the RGB controlers of the gamma equalizer and the gamma itself with the W controler of the gamma equalizer. The W controler does not interact with the RGB controlers --> the deltaE values don't change after using the W controler.
Source: Samsung UBD-K8500 (UHD), Panasonic BDT-110 (BD), Toshiba HD-XE1 (HD-DVD), Vantage VT-1S (SAT), Kathrein UFS-924 (SAT)
Calibration: LightSpace CMS, SpaceMan, SpaceMatch, CalMAN 5 Prof., Chroma Pure, Lumagen Radiance Pro 4446, Chroma 5, SpectraCal C6, EODIS3, i1 pro 2, Klein K10-A
Target: JVC-X7000 (Beamer), Panasonic TX-P65VTW60 (Plasma TV)
Sound: Yamaha RX-V2067 (AVR), Teufel Theater LT 3 (Speaker)