No, not in doo-doo for that, either. 😉 It’s still your primary residence.
Personally, I LOVE accessory units because they provide affordable housing in a way that doesn’t cluster low-income units in one area, which often cause higher crime rates and blight in the area. It also tends to hold landlords more accountable because most people won’t be slumlords when their rental is in their backyard.
As you’ve noted, the accessory unit is assessed at current market value (not sure about their exact formula, but seems to take construction costs and/or FMV into consideration), so you ARE paying market tax rates on your granny flat.
As for the ongoing Prop 13 protection that would cover the extra unit, I think that the benefits listed above, as well as the fact that you are building an additional unit (as opposed to just buying at existing unit), which benefits society by providing additional shelter that didn’t exist before, is worth the tax subsidy. Also, if the unit us used for elderly or disabled family members, this helps reduce the burden on public service members who are often called to check on elderly family members who live apart from other family members, or are called to help them get up off the floor, or help get them back into bed, etc.