I find that when you're using an IR heat gun the best places (at least on Ford blocks) to read temperature is on the right side towards the front at the head/block intersection. That represents the return coolant path in the block on those engines. I find at least on them the thermostat housing doesn't read very well... mabey gets a chill from air movement, etc... but along the right side is fairly sheltered.
Beyond that I'd have to wonder why you question the gauge? Most times if a gauge reads steady and predictably... it's probably good. You can obviously buy an electric gauge and mount it in an acceptable orifice... but electric gauges are somewhat susceptible to voltage variations in the system.
I don't think the muffler/manifold is going to have ~any~ bearing on the reading presented by the jacket temperature gauge you have now although it WILL effect the readings of an IR gauge.