First, an anecdotal observation from someone who spends as much time as possible going barefoot (even when running, or backpacking if the terrain allows it without slowing me down): I tend to strike more with my forefoot. I call this the 'tender-foot' walk even though I am not a tenderfoot, and this seems a sensible and natural way to walk barefoot on any terrain that is not perfectly smooth and soft. You will see Cody Lundin doing this a lot too, and he no doubt has really tough soles! But a forefoot strike would probably get pretty tiring to do for long days on the trail, so some protection for the foot allows more of a heel strike and longer distances at pace.
As for evolution, well, where to begin. As someone who is well past the age of reproduction, I can assure you that evolution really doesn't serve us well, as we can't pass on the genes for aging well. Our caveman friends probably did well to make it to 30-40 years, just long enough to breed and raise a family. Also, in evolutionary terms, humans branched off pretty recently from our ape ancestors, so to argue that evolution has had plenty of time to optimise homo-sapiens for anything at all doesn't make sense to me. Even in our ancestral environment, there was so much that could and did go wrong with our ancestors that to suggest we can't improve on nature's design for our well-being is something I strongly disagree with.
I'm not saying there is a right or wrong answer to flat shoes versus cushioned heel shoes. I would put this in the category of 'everyone is different' and do what works for you. As someone well past my reproductive years, I can assure you that one aspect of aging where evolution seems to particularly suck is that the fatty heel pad we all have in our youth, eventually thins, making the heels more sensitive to insults from the environment. As someone who has osteoarthritis in my ankle from a crushed ankle 20 years ago, I can also say that good shoe design is a god-send in that situation too. I'm pretty sure evolution didn't intend for my ancestors to even survive such a bad accident, much less be able to walk normally well into my older years. So in a waffly way, I'm all for going barefoot, and I'm all for comfortable modern footwear too, but none of this is thanks to nature's random genetic intervention in my ancestors gene pool IMHO.
And yes, even bare feet can blister, but I don't get blisters any more now that I figured out that, for me, wearing shoes too small (in length, width or depth) was the culprit. Shoes are tricky, and hiking shoes even more so, as you need to allow room for socks which are often thicker than you would normally wear, swelling of feet from just being on them for long hours, plus swelling from them being constantly wet, or hot, or that salty meal you ate the night before. Or 'that time of the month', or a million other things.
There is at least one good thing about being past my reproductive years...I no longer have to justify wearing ridiculous high-heeled footwear to catch a mate :)