That was my first impression too, that crush up and crush down should be simultaneous. If you only consider two bodies, that's the intuitive impression you're bound to get. It's only when you realise that the crushed material between the two not only can be, but has to be, treated as a third body that the rather more counter-intuitive result becomes clearer.
Firstly, the two frames of reference aren't equivalent, because the reference frame of body 2 isn't inertial. It shouldn't be surprising, therefore, that the results aren't symmetrical between the two bodies. Secondly, there's the rather major asymmetry that body 2 is fixed at its outer end to a mass large enough that it may be treated as immovable, whereas body 1 isn't; body 1 can therefore move freely under the action of the forces acting upon it, whereas body 2 can only crush.
That depends on what the assumption of a rigid body actually means. In this context, it means that elastic and plastic deformation of body 1 is negligible, not that body 1 is indestructible. Body 1 is still allowed to crush; the absence of crush-up is a result, not an assumption.
Nor was it ever intended to be a sufficient explanation. It is, rather, a limiting case. There is an infinite range of possible collapse modes, with varying energy balances. The BZ calculation is based on the one collapse mode that is most optimistic to survival; however unlikely that mode may be, if it is found to result in collapse, then any other collapse mode must also result in collapse.
In reality, it's perfectly clear that the impacts were not column-on-column; it's likely that there were several processes going on simultaneously, including funnelling of rubble into the inside of the perimeter column tube, floor collapse, and buckling failure of unsupported column sections trailing the interior collapse. There's also the role of the hat truss to consider, in presenting a stronger top end of the falling block and quite possibly doing considerable damage to the core as it collided with parts of it. However, what we can say with reasonable certainty is that the real collapse mode was energetically more favourable than the theoretical limiting case analysed by BZ, and that therefore global collapse was the expected outcome. Detailed analysis of the collapse to show that it differs from BZ in fine details is irrelevant to this conclusion.
Dave