...also, so you are saying if the engine has ran for periods of time with water, or improper mixture it is more prone to getting those low spots? even if when it was rebuilt the original head was resurfaced?
Coolant that has become acidic because it was wasn't changed every two years, or if incompatible types were mixed (including if types were changed without FULLY!!! flushing the old coolant like six times, including flushing the heater core), or if tap water was mixed with the coolant, then the acidic coolant tends to rust the sealing rings of the head gasket, as well as corroding the iron block.
Rust in the coolant galleries inside the block is not a great thing, but doesn't necessarily affect the head gasket surface. But if the coolant manages to rust the head gasket sealing rings, then the iron block surface immediately below that rusty ring is also probably rusty, and that can create a low spot.
Sometimes it's hard to test that low spot since it may be more narrow than a feeler gauge. Trying to shine a light under the straight edge may be a better way of seeing if there is in fact a low spot; of course that won't tell you how low the spot is. Graphite does a good job of sealing small imperfections, but if the low spot is directly under the steel sealing ring of the gasket, you really should have the block milled.
Good luck with it, and post some pictures if you can. It's always interesting to see what things look like in there!