What the deuce is a QI charger, what do you mean? What's Cyanogenmod? What do you mean the USB port will fail? And I don't think a QI charger would even work with a 2012 Nexus 7, maybe a 2013 model.
Is this the TWRP thing you were talking about earlier? http://teamw.in/project/twrp2/103 I assume it is, so it's on the Google Play store? Weird lol. Anyways, my only reason I'm concerned is one, this is Christmas gift, and two, these are bloody expensive, I don't want to know how much he spent for a new one of these, that's why.
It is yeah, there's an alternative as well called clockwork mod.
I understand your concern especially if your not tech savvy but it really isn't too hard to do with minimal risk involved so long as you follow instructions, I've had one phone brick on me.... ever and even then 20 mins later and a stock ROM it was working again.
If you wanna do twrp from Google store which is more than safe to do, you would need to root first as the app would need that level of access. Google and manufacturers are on record saying that they have no issues with people loading custom roms or rooting devices but it would void warranty, again easy to work around with a clean stock ROM. The only company I've ever known to restrict this type of access is HTC.
Obviously your call whether you want to go ahead with this, just want you to know it is easy to do and comes with very minimal risk, I've rooted countless android devices and even do it for friends if asked to