Overly cheap parking is a problem for sure, but so is overly expensive parking. The articles you cite say that an 80-85% occupancy rate for parking spaces is most desirable, a figure I've seen before. Say the city determines that for every dollar parking is increased demand drops 10% and at $2 an hour demand is the optimal 80%. That means that the market is most profitable when parking spaces are actually $5 an hour and demand is 50%.

In the closed world of parking spaces $5 an hour is the optimal rate, but in reality this could be disastrous for traffic and business who are now dealing with increased congestion and reduced customers respectively. Taking the ability to set pricing out of the control of the city and placing it with independent/selfish actors might have unforeseen ripple effects on the wider community. Therefore it should well within the city's right as an actor who is responsible to the community to direct the use of its property as best suits the public good.