Turned out I had two misconceptions:
That i-frames (i.e. invincibility frames by damaging self on spikes) were required. They're not.
That the shortness of the hop had something to do with it. Nope.
The trick's execution only requires these steps:
Jump, any height—no need to hold.
Tap Down anytime during jump so Samus points her gun down.
Tap Down again the morph just before landing on the platform / Kago.
Similar to a machball (mockball) without the horizontal movement or holding A.
How does it work?
Samus's morphing animation is uninterruptable by the game. Therefore, if the animation is initiated just as Samus is about to land on a thin-enough platform, the game will miss its chance to do collision-checking. This technique works on Kagos, for example, because their membranes are thin—it's highly recommended that you practice on top of these, first. The technique also works on the spiky platforms ("Kzans") in Lower Norfair (as shown in the video), as well as the yellow robot-like platforms, because the actual "steppable" region of these platforms are thinner than a full block (16 pixels).
Okay, then why run into the spikes?
This actually turned out to be a health conservation strategy. The spikes on the wall do only 15 damage, while the spikes on the underside of the platforms (known as Kzans) do a lot more—40 or 50. By gaining i-frames from the former, you avoid hurting yourself Kagoing through the latter.
Why the short hops?
No reason, besides the obvious fact that the ceiling is low over the Kzans. It might also make the timing of the button presses easier when the hop is short.