I think most of what we feel as flex is really explained by the steering geometry and interaction with the tires. The bottom bracket does flex, no doubt about that, but I don't think that is the most significant reason that the bike feels like it is flexing.

I saw shimmy was mentioned. Shimmy is a rigid body motion of the wheel/frame and does not involve vibration modes of the frame. We measured the first natural frequency of a frame and it's significantly higher than what you see in shimmy. Shimmy generally seems to be exacerbated by having weight further back on the bike, you have to take that into consideration while touring.