I agree with you that those are normal things for a public transit agency.
I felt like the core of the article was that NYC had ignored an established pattern (outlined in a report[1]) that suggests that, for this to work like they want, they would need to increase non-car ways of getting into and around the city. I also thought the article did a good job of talking about how the legally relevant metrics are focused on financial targets rather than transit targets.
I do think this kind of article is hard to write clearly, but I do not think what you said is in conversation with the content of the article. I can see why they are worried that congestion pricing must fund new capital projects (i.e. expansion) instead of the existing system. You didn't mention that in your critique and I'm curious because it feels like a central point of the article.
I also do not think this article was exactly criticizing the MTA for overpaying? More than it was noting that it HAD overpaid to situate the reader as to the MTA's current financial situation.
[1] https://rpa.org/work/reports/congestion-pricing-in-nyc#key-f...