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I'm no pro, but maybe that was from a machinist's previous screw up? If it's been like that, it should continue to be fine. Assuming umbrella type seals are going to be used.
What heads are they? If they are later peanut port heads, it is a good excuse to find a better seat of heads.
Those have some heavy duty inserts on them... I would think that you might be alright, but you can replace the whole guide if it makes you feel better. I had to replace one of the guides on mine when I busted it while installing a liner in it.