That's the problem with the regular Par64 LED fixture. If you cannot specify that the fixture must have at least channels 1-3 set to "0", then you cannot effectively blackout the fixture (say from a color-mixing standpoint). If you are using the built-in color macros, then you can probably just use the dimmer channel.
In order to completely utilize these fixtures in all of its capacities, you need a controller that allows you to specify "ALL" as a channel/value for a blackout or even a grand master fader. Many controllers do not allow for something like this (including some software-based fixture profiles).
I believe the Par64LED-PRO takes care of all of these issues (but don't quote me on that). I guess for some, the regular P64 LED works great in DJ/Auto settings, and for those who need more finesse and are far more picky (like myself), get the PRO version.
It is just something that could have been solved if the fixtures were designed such that the DIMMER channel actually did just that, act as a dimmer, but it really doesn't. It's just more of a pseudo shutter-like emulating function.
To me, a dimmer channel should equally affect all channels that produce visual output from a fixture. In conventional fixtures, this is easily accomplished by dimming the lamp, and the entire source of light is controlled.
With LED/color mixing fixtures, multiple channels produce output for the unit, therefore a dimmer function should affect/override all of the channels that produce visual output (i.e. channels 1-3, etc).
To me, the entire situation just creates a significant hassle and requires me to bend over backwards to accommodate the fixture.