I've ruled out the bottom bracket. When the bike came to me it was a bare frame, and I put in a Shimano cartridge BB in with a nice straight spindle. Early on in the diagnosis process, I swapped the BB out for another, higher quality Shimano cartridge unit, also in very good shape. Flex continues unabated.

The cranks are also in good shape, I had them on another bike and there was no problem. When viewed from above, chainrings look nice and straight as crank turns.