Hi rbev2308,
Zoned cores can be made with a zoned mold, with fabricated sections, or with various cut outs or surface modifications.
Zoning can make either a small or a significant difference in alignment depending on the specifics of the zoning and on how well it matches the needs and preferences of the person on the mattress. Zoning is typically done with support layers (innersprings, polyfoam, or latex) although it can also be used with comfort layers and it would certainly still have some effect with a 3" comfort layer over it although again it would depend on the specifics of the zoning.
Comfort/pressure relief is what you feel when you first lie on a mattress and support/alignment is what you feel when you wake up in the morning and zoning is usually more about alignment than “comfort” although it affects both because it allows for the use of softer layers under pressure points.
There is more about zoning in this article and in post #11 here.
Phoenix