From what I've gathered, the additional fee is designed to incentivize developers to include at least 20% affordable housing units in new projects. If you're building less than 20% affordable housing, you pay a sliding-scale fee. That money goes to supporting staff in the city that monitor and enforce affordable housing regulations.
I can definitely see the opposing policy argument here: just remove incentives on developers and let the market figure it out. However, I don't think Item #53 is some kind of scheme to keep housing unaffordable on the part of home owners.
I wasn't able to find the de-zoning item in the agenda, if anyone knows which one it is I'd definitely give it a read. Full agenda here: http://www.ci.berkeley.ca.us/Clerk/City_Council/2017/06_June...