cylinder head coolant temp is a function of both coolant temperature and combustion temperature, as the heads are a fairly direct heat sink for combustion heat.

just 'cause your coolant sensor is in coolant doesn't mean it doesn't measure the heat of what it's threaded into as well.

the intake is not a direct heat sink for combustion temperature. as such, coolant temperature in the intake is much more consistent with coolant temperature.

so these results are not suprising.

headers shouldn't make a difference, nothing bakes a sensor like tightly fit cast iron manifolds

having the ECM's temp sensor in the head is weird to me, most of the time in a factory configuration it's in the waterpump or intake or something, and your gauge sensor is in the head (not that it really matters where your gauge sensor is, it's just a gauge)