Why the specific root of the Other Side lies in the world of Nekudim.
The Other Side is rooted specifically in Nekudim because the cause must match the effect-level. The law of gradation requires it.
Op. 43 said evil is rooted in Beriyah, Yetzirah, Asiyah (BYA), not Atzilut. Op. 44 sharpens further: why Nekudim specifically and not, say, generally throughout BYA? The answer invokes the law of gradation — a structural rule that runs through the entire book.
The law of gradation: the cause of an effect must match the level of the effect. If you want a particular cosmic outcome, you need a cosmic cause at the appropriate level. This applies generally: a high-level outcome requires a high-level cause; a low-level outcome requires a low-level cause. Bringing about an effect at level X requires acting at level X (or at a level that can directly produce X).
For the Other Side to exist as a real cosmic structure, its cause must be at the appropriate level. The cause is rooted in Nekudim — the successive (un-integrated) state — because that is where the conditions are right for the parallel structure to come into being. Atzilut is too high; the lower portions of BYA are too far downstream; only Nekudim has the operational state that produces evil's root at the right grade.
The law of gradation generalises throughout the book. Op. 14 (the cosmic configuration is exactly what the goal required); Op. 116 (CHaDaR runs through Zeir Anpin (Z"A) because this is what is required for the cycle of six thousand years); Op. 138 (the eight-stage Coupling order is what the operational mode requires). Each is a specific application of the same gradation-rule.