That article is faulty in assuming that there was not the potential for variation in the orignial bacteria. Until scientists fully understand all of the bacteria's code and how it functions, they cannot claim that variation only comes from mutation and was not already inherent in the code in the one bacteria.
It's not sufficient to say they all came from one chromosome, because until you understand the functionality of recessive genes and all DNA (previously called junk DNA) you can't claim that the variation is exclusively mutations.
Nevertheless, I'm not saying variations don't arise from mutations, just that most of those are negative.
But I agree let's move on.
How many mutations have you counted? And how did you judge them to be positive or negative?