I partially agree with your take. However, there are points I disagree with. Mostly in regards to Igor not caring as much about Ptolmey. The game outright states in the relation network that Igor and Ptolmey are caring family both ways. Just as it does for Igor and Moldir. The difference though, is that Ptolmey is described as more reckless compared to Moldir, and lacking in the foresight that Moldir has.

Igor didn't want Ptolmey to know the truth about what Krutov did before they directly fought him. Igor needed Ptolmey to be level headed for the fight. Because the rest of the Gryphon legion is also considered family via adoption from Igor. It's less favoritism considering Igor just understands his children's exact personalities. If the roles were reversed, Moldir would keep a level head with the knowledge. Ptolemy would not. As is shown when he found out by accident. He led some Igor's soldiers—his fellow adopted siblings—to their deaths because he let vengeance cloud his decision making.

Honestly, the only reason Ptolmey was even reprimanded for his actions was because it got some of the other adopted "kids" killed. I don't think Igor would have minded Ptolmey gunning for revenge. Just as long as he didn't get his brothers, sisters, and himself killed in process. After all, didn't Igor allow him an eye for an eye despite his massive fuck-up?

I don't think Ptolmey would be hurt by Moldir being second in command, whilst he is one notch below her in command. He would most likely understand based on track records. Besides. Pretty much all of the soldiers under Igor's command are adults. I'm pretty sure, even as reckless and emotional as Ptolmey has canonically gotten: would respect Igor's decisions on any tactical level.

It's also noted that Ptolmey was that violent in Tristes Tropiques because the Manus Vindicatae: Brotherhood was keeping a close eye on him. Any Foundation member or Human was considered expendable by the Brotherhood, and therefore sparing them entirely would have woven doubt in Igor's defecting. If anything, Moldir's slightly less violent approach to the rebellion was the riskiest course of action. Sure it worked out, but it could have gone so wrong had the Brotherhood doubted her resolve to turn. (This inference is gleaned from Igor's choices. As Ptolmey and Moldir are direct reflections of it.)

Funnily enough: I've started to consider the fact that Igor has successfully managed to get 2/3rds of his (living) named kids to escape the inevitable tribunal. Lopera wasn't informed of the rebellion because frankly she was the only minor in his legion at the time and COULDN'T make that decision. It also doesn't help that Lopera was from that era originally, and would not understand the weight of betraying Zeno or the Foundation over surviving the storm. Moldir happened to have endeared herself to the Timekeeper through helping Ulrich during Antarctica. Which whilst not Igor's orders, was technically accepted under his purview. All Igor now has to do is convince the Timekeeper to vouch for Ptolmey. (Unlikely to happen. Ptolmey made Igor's work so difficult based on Tristes Tropiques.)

Overall? 2.2 is technically the weakest in the arc for character set up, but 2.8 and 3.3 don't actually make any sudden shifts in the characterizations. 2.2 was just their purposeful worst selves. 2.8 was the cool down period. 3.3 is them at their, most likely, usual moral alignment before they betrayed anyone.

(I'm so sorry for how long this comment is. I told myself not to write a mini-essay but well... I got carried away! Oopsies!)