There’s 2 main reasons to only apportion a certain % of units as “affordable” while Maintaining a majority as market rate.

First, ideologically HUD and many advocates have pushed the idea of deconcentrating poverty. The old way was to build large tracts of subsidized housing in undesirable sections of urban areas. You can see this type of development all over (parts of) town. Most of that can’t be undone, and it can be very difficult to put together a funding stack for something that isn’t 95-100% subsidized, affordable. The newer idea is that the “poor” will have better outcomes if they are mixed in all together with other economically diverse families rather than segregated. This is some of the idea behind rental vouchers as well, but as we know voucher holders struggle to break out of economically depressed sections of town too. Having a small to medium % of units in a new construction can be a really good way to further deconcentration, depending on the particulars.

Second is money. Even with millions of government dollars, it is really, really expensive to build this type of housing, a cost that is compounded often by the strings attached to that government money. Government money that usually only makes up a minority share of actual costs. Eventually a building has to generate enough income to both pay staff and service the inevitable debt on the property as well. Additionally, “non-profit” doesn’t actually mean the organization doesn’t make a profit, it just means there’s a socially beneficial bent and the profits aren’t distributed to any kind of shareholder, they stay with the organization to further the mission.