This small amount of bolt head under turn is very common when fitting bolts. Its been noted in previous posts that armourers had a "bolt head spanner" usually made up during their apprenticeship that was used to work the bolt head until it just aligned with the bolt rib (best) or over turn by a degree or two (good).
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Like this ?
Mine are not the best, but they are not too bad. I can think of lots of Enfields I'd rather have but instead of constantly striving for more, sometimes it's good to be satisfied with what one has...