A great discussion of a Gene Wolfe story that is one of my favorites — if by "favorites" you mean "I'd include it in a best-of volume", not, say, top 3. Still, I'm surprised it didn't make Best Of. I think you did a very good job on the story's politics: far less standard conservative than we've seen before, seeming both anti-war and environmentalist, although of course those are two areas where we've seen Wolfe have leftier-than-on-other-things views in the past. Still, the overall effect was a critique of American imperialism, both in Vietnam and in the natural world.
You didn't mention one of my favorite bits of humor in the story: the way that Wolfe described what makes the gestures, and then later just describes the gestures; thus, the superb, free-standing line: "Dondiil parted the hair on his body horizontally." Incidentally, one of you mentioned (in analyzing the ending) that the story is largely from Quoquo's point of view; but the explanations of these ("the conventional way of implying...") indicates a more distant-third person than that suggests. Given Wolfe's utter willingness to inhabit the world of his characters—and not explain—when he wishes, I think this is possibly significant.
Overall, I had a far more literal reading of the story than you did. First, I saw nothing in the story to indicate that Dondiil is pranking Quoquo. I get that it sounds like an army prank to you, but I just don't see it. They're not in the army (as far as we know), first of all. Second, Dondiil comes across as slightly subservient, even obsequious, to Quoquo — and while you could read that as motive to prank, I also assume he wouldn't dare. So I took it straight: the tigers escaped.
Then there's the last line. This, I admit, is more ambiguous than their escape. But led me adduce one piece of evidence you didn't mention: a seemingly-casual, but possibly-important early simile: "the skyacht would have looked surprisingly like a phoenix as the flame from its rockets washed backward over its own indestructible skin, had there been any eye watchin to which the phoenix was known." First, this is another example of distant third, not Quoquo's pov-third, in the story, But more importantly, the phoenix — shoe-horned in in a way that both highlights the absence of humans and the simile itself — is both a mythical beast, and one that returns from the dead. The former could be taken as implying the eyes at the end are simply Quoquo's imagination, I suppose, but I find it much more likely that the simile implies the opposite: that the humans have returned from the dead (not always survived, as you speculate), and that it is because of some mystical connection between them and their land's mythical symbol, the tiger, being returned from the dead. I think this story is, in its own small way, a "Frankenstein' story, about people whose technology come back to haunt them — as well as people who are messing with forces that they don't understand. All this, of course, synchronizes nicely with both the narrow Vietnam-war angle on the story and the larger critique of American (really, broadly capitalist) imperialism.