Why wouldn't Skadi be able to save her Def down for W3?

It's not about saving. It's about the second Skadi not being on the field anymore because you switched her out for Waver.

You start with two Skadis in W1, use both their Quick Buffs and one 50% charge. You NP. Zerkerlot regenerates ~32% NP (on Sabers!) assuming no Overkill hits bar the killing blow.

W2 starts. You use one def down, then switch out that Skadi for Waver. You give Zerkerlot 20% charge off Waver and 50% charge of the second. You also activate Zerkerlots NP generation skill. Zerkerlot NPs. He regenerates 63% charge (again, no OK hits bar killing blow, on Sabers).

W3 starts. You only have 30% charge of Waver left. Oops.

You already see how this setup is unstable already now. You already require Overkill hits, despite switching a Skadi out and using Wavers charge skills in a more flexible way. If you use Wavers 50% in W1 (instead of one of the Skadis), this problem is only getting worse. And if you're fighting Berserkers or Assassins, you regenerate even less charge.

That's why you don't have two Skadis in W3. You need to switch one out, otherwise this setup doesn't work at all. You need to spread out Wavers charge over two waves and as such, you can't simply switch Waver out. In this case, you don't need to see Waver and the Skadis as 3x50% charge but as 2x50%, 1x30% and 2x20% and you need to spread the latter to make it work.