I haven't seen evidence that manipulating skee-ball machines is a common practice by owners, and I've played at a lot of places. Several of the modifications you mention aren't easy to make. (At least, I can say that's true when it comes to the official machines made by Skee-Ball Inc -- I usually avoid the knock-offs so I don't have much experience with those.)
I was saddened to learn that the company was acquired by a rival earlier this year and relocated production from the Philly suburbs (where it had been over 100 years) to Wisconsin. Strangely, no mention of any of this in the article.
It doesn't seem like there should be much incentive to manipulate the skee-ball game itself since the owner can just adjust the ticket payout to meet a pay-out %. Since skee-ball has "high entertainment" value, i.e. the player has fun playing, the payout can be lower:
I'd also disagree that skee-ball is a game of chance, because at the least, it's a game where how well you do is determined almost entirely by how well you roll the balls. And it's not a game, like a ring toss game, where you have to get lucky to do well.
I've played skee ball at a couple places where it really is a "pure", fair, game and it's a bunch of fun. I can imagine less ethical places doing the things you've suggested, though I've never seen it myself.
It is fun to play once in a while, I'll usually do a few rounds every time I go to Cedar Point. But it is subject to the same machinations as all the other carnival games.