When I first certified in Control4 I was fairly astonished to find the remotes didn't have IR built in, but at the same time very relieved! I've enough experience in AV and other control systems to know that relying on the end user to point one thing at another for any longer then 500 milliseconds is a bad idea. While you may not get any issues sending the odd command, start sending macros and eventually something will miss. As RyanE said, its simply not reliable.
In terms of "Backup" 95% of systems we install have a HDMI matrix in place, we then have a IR receiver at each TV, and a bud on each source at the rack allowing direct control using the original remotes. This IR backbone is completely separate to C4.