I've never seen it on a stock block. Yes, having it cut with the block is ideal. The issue is a little less critical with a composite HG than with a metal HG as the composite has a some elasticity and will fill in MINOR imperfections. The head gasket overlaps the timing plate and the excess height may cause issues. Over cutting the plate a little isn't a huge deal as it's just an oil galley. Dress the HG on both sides with a good sealant (Honda FIPG, The Right Stuff, etc) where it meets the timing plate and where the timing plate it meets the block (as specified in the TSRM) and you'll be fine as well.... But yes, at the end of the day getting it cut to match the block is the way to go.
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