Bill Houghton, Sebastopol, CA
David Pye (1914-1993), an English professor of design, argued that irregularities were inevitable when doing work guided by hand*, and that these irregularities were what made work attractive and human. He was writing in the late 60s, and was NOT a fan of extravagantly and deliberately irregular work - I believe his phrase was "lumpy pots and hairy shirts." In effect, he was arguing for doing work as well as possible while realizing that irregularities would be present.

I think adopting the practices of folks back when hand tools were how work got done is likely to be the best approach. Instead of cutting everything to a measure then putting it together, cutting everything to fit the next part over, for instance.

Myself, I like to see work with subtle signs that a hand, not a machine, made the piece, rather than something that screams, "Hand tool work!"
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*You may be familiar with his distinction between "workmanship of risk," work guided by the craftsman's hand and skill; and "workmanship of certainty," work guided by jigs and fences that allow for no deviations.