I've had a number of the problems you see on various forums, and probably the problems CR is talking about.
Faulty dash lights? I assume they are talking about an issue I've seen on forums a lot, and several times in my own car. After charging on a level 2 charger it will often throw all kinds of warning messages and lights. Once, it wouldn't even start for about 10min after charging. I'm pretty sure (I'll have to check) that one of the recalls was supposed to fix these issues. Don't get me started on the Android Auto and Honda Link apps (both through the phone and accessing them from the car infotainment screen).
Climate controls? I don't remember the specific issue, I've never had it, but I did get a climate control related recall notice a month or two ago (and just had the recall work done yesterday). I assume the recall issue, being climate control related, is what CR was talking about, and I assume the recall will fix it.
Trunk lid issues? I really haven't looked online to see what kind of problems people are having. I do know that when I unlock and open my door and start the car I sometimes (once every week or two) get a warning light that the trunk is open. I'm not hitting the wrong button on the key fob because I'm not using the key fob. I'm unlocking with the door handle with the key fob remaining in my pocket. However, all it means is that I have to get out of the car and close the trunk before driving.
The first is annoying, but always seems to fix itself pretty quickly (the more serious one anyway, not the issue with the two apps unfortunately). The second hasn't affected me, and hopefully the recall fixes it overall. The last is nothing but a minor annoyance.
My take is that it isn't as trouble free and reliable as I hoped a Honda would be. I am a bit peeved, but it wouldn't stop me from recommending it (or buying it if I was to start over- though I'd possibly consider one or two others a bit more, especially an all electric with several 200+ mile options now). From reading, the Clarity and many other recent Honda models seem to have similar problems overall now. However, they are still bullet proof mechanically. So, minor livability issues but the car will likely last forever... I'd rather not deal with them, but it isn't the end of the world. It does make me a little nervous going into the future, but I'll keep an eye on it and hopefully it will be fine.
As for CR, I'm pretty sure it is these livability issues that got the Clarity its rating. I think they should weigh severity of issues much more instead of looking primarily at number of issues, but I think they look more at the number of issues. If that is the case, again, a few annoyances but otherwise a mechanically sound car is much preferable to one that all its software works right but will break down and leave you on the road, or will die altogether in 100-150k miles.