"Almost no resistance" is relative. The 85 floors or so offered enormous resistance. So much resistance that it was capable of holding a whole (peacefully standing) skyscraper up. But this resistance was dwarved by the dynamic load of the falling upper section, which was even ... well, enormouser.
I could defer you to the calculations in the paper, but I sense that the problem you're having is that you can't reconcile the progressive collapse with your "gut feeling". So I'll try to explain with a very simple model that you could grasp more intuitively.
Let's say that one floor (floor A) fails and the upper section falls the distance of one floor. When it hits the next lower floor (floor B), it will have speed v
B-enter. Now, floor B either a) has enough strength to brake the upper section entirely to a halt, or b) it does not have enough strength. In case a), the falling section is halted and collapse is arrested.
In case b), floor B fails. It may have slowed down the fall of the upper section, but the section continues with non-zero speed, v
B-exit > 0. But this means that when it falls another one-floor distance and impacts C, it will have greater speed than it had when it impacted floor B. This is because the first fall began with zero speed, but the second fall began with greater speed, v
B-exit. So floor C will be hit with speed v
C-enter > v
B-enter.
Well, if floor B couldn't halt the upper section impacting with speed v
B-enter, floor C is likely not going to halt it impacting with speed v
C-enter > v
B-enter. So it will fail, and slow the fall down to v
C-exit. And, if floor B slowed down v
B-enter to v
B-exit, it's only logical that floor C will slow down v
C-enter > v
B-enter to v
C-exit > v
B-exit.
And so on. Note that we didn't even consider that the mass of the upper section was increasing; even if the floors vaporized upon being crushed, the collapse would still progress with increasing speed.
This is of course a very simplified model. It would, for example, be different if the initial falling distance was greater than one floor. In such case, it would be conceivable that the collapse could be halted even after several floor are crushed.
But basically, it shows that either the collapse is halted very early in its beginning, or it's not halted at all. Once the fall begins to
accelerate, meaning that the floors fail to slow it from floor to floor, there is no way to stop it - until the upper section hits something much firmer, that
will be able to halt it (such as the ground).