In other spots of the movie the red was used and mixed with film at very high quality ... from that link I gave before ... here's some more info:
“Once the original scene lighting is programmed into the dome, we bring in the hero actor,” continues Williams. “The hero actor sits in a stationary chair (with slight head restraint) and recreates the performance that is being played back on a reference monitor. The recreated performance is recorded with four RED EPIC cameras placed strategically around the dome. The final step involves projecting the RED footage back onto a cyberscan of the hero actor’s face that has been 3D tracked back into the original scene.”
That approach has been used for almost 10 years now, using HD cameras at first and higher resolutions as they became available. This is largely based on Paul Debevic's work and as I recall was used as early as 2003 on "Matrix Reloaded."
BTW, any time you hear that projection mapping is the "final step," be aware that this is rarely the case. All of these type of effects are tweaked to death and often fixed by hand, because those "automated" approaches rarely work as seamlessly as many would like to believe - and that very much includes the 3D tracking of replacement objects.