You'd like to think they're independent and fair, but thats kind of the whole point of the article.
To quote the state director in the article “I don’t think we’ve ever represented that the auto-hold gives you the optimal result,” he says. “The idea was that it gives you a good result.”
You'll get a perfectly good result if the lotto balls are loaded. Might not be optimal, might not be random, but it'll be a good result, as in not some random negative integer or a float or wrong number of balls.
I agree with you that lottery might make lotto draws unfair. For example, they see in advance which combination of numbers is NOT played and somehow they cheat and draw exactely that numbers. Lottery can do that for several weeks in a row, thus making the prize pool bigger and bigger and atmosphere between players hotter and hotter. As a side bonus, lottery can use fresh cash (from stakes) for several weeks at 0% interest rate.
But, can they really do it? Manipulating lotto balls and drum (mechanical devices really) is much harder than manipulating software behind some video poker game. I don't say it's impossible, but harder.