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what is the typical accepted coaxial tolerance
Dunno, a bearing manufacturer will have tables for that kind of thing. Since the bearing separation is about 10 times the bearing radius, you will want the axis of one bearing to intersect the plane of the second bearing inside a circle with a radius of about 10 times the maximum permitted clearance on the lifted side of the bearing and centred in the second bearing. I think I'd want the target circle to be R<50μm just to make the bike somewhat ridable and durable.
The further out you are, the more the bearing bears on only a subset of the rolling elements as the inner race is canted relative to the outer race. This is a perennial problem in designs where the bearing seats cannot be cut with a single tool without moving either the work-piece or the spindle axis, and for this reason designers try to avoid such layouts. For example, the circlips in a BB30 bottom bracket seem like an annoying and unnecessary complication compared with just machining a shoulder into the shell, but they make reaming the two bearing bores coaxial a piece of cake.
what is the typical accepted coaxial tolerance when using (for example) IS41-compatible bearings? I can't imagine that I will end up with more than 0.1mm dislocation over 200mm headtube length, and that should really be fine? Also given the fact that (as you said yourself before) components generally deform under load here and there.