Ok, so my earlier post was speculation from my desk at work. I had a look at my 600EX-RT this evening, and the way it works is this: there are two little 'windows' on the bottom of the flash head. One is an emitter, the other a detector. The bottom of the holder has a little prism that reflects light from the emitter to the detector, and the light passes through the tab on the gel. The little metal disk next to the prism on the holder activates a magnetic sensor in the flash, so when you mount the holder, there are a few flashes of light from the emitter (a small white LED, probably) - if you look from the side when you mount the holder, you can see that happen.
Now, having said that, the statements in the manual may be Canon CYA language, not wanting to take responsibility for you getting the wrong flash temp and thus WB in the EXIF. The system may actually do ok, and it's worth testing. Looks like the gel color is determined only when you first mount the holder, then stored. For the color check, it seems that the gel only need cover the prism at the bottom, so you may be able to empirically test the WB setting with your non-Canon gels...