But if they're doing a historically accurate repair or replacing timbers, or a reconstruction, wouldn't they use timber that was irregular if that's what the previous was?

Jörn Wingender's article on German Timber framing in Timber Framing #48, page 6 shows "Wild man" curved timbers and states: "Straight,fast-growing spruce began to replace the dominant
'old-growth' oak and beech forests in the 18th century.
Timber framing was already in decline when
these trees reached maturity. Scribing remained the
prevalent layout system until the disappearance of the
craft as it was known." Maybe scribing was forgotten, but it's hard to think they would replace the bowlegged Wild Man with straight timber on a historically significant building.