Your right the Nightsisters arc requires the least amount of meddling of the first batch. I’d say the three parts could work perfectly fine as a single episode (this way “501st Legion” doesn’t feel like the only black sheep with 50 minutes of runtime). Monster is the one that, as you say, would require the most trimming around the middle section. On first thought I don’t really agree with cutting the Toydarians as I don’t find their portrayal problematic (I’d say it was a saving throw from the producers to set them apart from the stereotyped, divisive Watto), but if it works better for the pacing (and also because Katuunko doesn’t feature in other Continuity cut episodes, so a first-time viewer wouldn’t have any connection to him) I can understand shortening that part.

Regarding the context of the episodes, you’re right that you could set a precedent with the Separatists striking at crucial targets. Christophsis in Legends was a flourishing mining industry with a strategically important position in the Corellian Run hyperlane. You could state that the resources from Christophsis helps fuel the Republic’s shipyards or weapons divisions.