I just talked to CPS Hollywood the other day and got into a conversation about what 3rd party accessories I should get, and they warned me not to use any 3rd party batteries because they might blow up in camera, I told them I've been using Canon DSLRs with only 3rd party batteries for about 10 years and not only have I never had that happen but I've also never heard about it either but the lady insisted that they have seen it...
I don't mean to be an alarmist but now with this extra warning in camera about 3rd party batteries and the fact they tweaked the camera to misread some chipped 3rd party batteries I can't help to wonder if they did something that might make this happen :/ like no longer restricting something on the higher capacity aftermarket battery. I've had batteries from other stuff blow up on me before (an Apple Macbook, an Avid portable M-Audio recorder and a few cellphones) they just bloat up and no longer work.
This is probably just some marketing trick to scare me into giving them more money but I wouldn't surprised. (who the hell is running Canon now a days anyway?)
I think its part alarmist, part reality. Canon can't QC third party battery manufacturers. While I'm sure a quality 3rd party battery vendor wouldn't put out a failing product, thats not stopping some cheap knock off vendor from providing batteries for canons and users purchasing them. All it takes is one battery failure and canon is correct in their assessment. And considering all the battery options I see on ebay, I see it more a likelihood that a user would buy one just to save a few bucks.
If you are going to spend $3K on a camera, a $70 battery is part of the cost of doing business. Playing lottery with a microprocessor controlled power source is a risk.
If I put out a pro product, I'd definitely put out a boilerplate statement about using OEM accessories just to save me the pain. Sure OEM cost more, but you are paying for reliability.