I think the key point the article makes is about the fee in lieu. It is kind of a sneaky mechanism to make it look like the program is providing a bigger incentive than it is while giving the city a new funding source.
While many folks are not aware, the property tax has always worked as described in the article. A levy value is set and gets collected. Various state and local tax exemptions re-distribute the amounts due by taxpayers but the amount levied is collected from the the base of property owners by increasing their share. This has always been done that way.
This expansion of the Multifamily Tax Exemption (MFTE) to questionable projects with no guardrails to ensure there actually is a benefit for the remainder of the taxpayers who are shouldering the load is weak at best. The fee in lieu makes it worse- like a secret tax increase done behind the scenes.
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