raw food

But we're not discussing raw vs cooked food here, are we? The article in question and the "articles" they sourced claim microwaving food is an inferior method of cooking than other traditional methods. Though, human evolution tends to agree that cooking your food is simply better.

but it was being argued here that microwaves may uniquely cause damage over other methods of cooking.

So the proper scientific way of proving that would be to cook the same food on the stove or other methods and test their difference in nutrients, which the article does not do by the way. You can't claim that the method does something different from the others without testing said methods too.

it should be fair to at least consider it uncertain if microwaves are healthy or not; it sounds like people should avoid them when they can, but if they want to take the risk, that’s for them to decide, and there should be discussions on if it is healthy or not.

If you're not going to believe the other studies and articles saying the opposite, then it's your freedom I guess. But consider this, I could change your quote into "It should be fair to at least consider it uncertain if cooking on a stove is healthy or not; it sounds like people should avoid them when they can, but if they want to take the risk, that’s for them to decide, and there should be discussions on if it is healthy or not", but would it still make sense to you?

plants given microwaved water did not fare well

I don't think that's really relevant to the topic, as humans have multiple organs to fend off harmful substances while plants have none. As for the article itself I can't comment on it too much, but a sample size of 2 is still too small, and ideally the experiment should be conducted in a way more controlled manner including a controlled environment, controlled source of water including not heated, heated, and microwaved, with maybe sources varying from tap water to diluted water. The problem could very well be the water source itself and not the microwave, or the plant itself was already dying regardless. And a quick Google search of "plants microwave water" gives me other articles debunking the myth, so that doesn't really help.