I think I have an explanation for the Luxury Ball having a normal catch rate but making a Pokemon happy. The internal circuits are specifically designed to create a uniquely comfortable environment for whatever Pokemon gets caught in them. Thus, when a Pokemon gets sucked in, all it feels is the “default” environment. However, if it lets itself get caught, the internal circuits “read” the Pokemon’s preferences and arrange a uniquely satisfying environment for it.

(Note for readers: this question is in reference to an ongoing problem, raised by my belief that Pokémon can only be captured if they are willing to be partnered with humans and that the process of battling is more about winning a Pokémon’s respect than beating it into submission)

Well, it’s probably imagined to be something like that, yes, the reason that it doesn’t affect the capture effectiveness being that it works more slowly and can’t provide that nice environment instantly, while the Pokémon is being captured.  Working out what Luxury Balls seem to do isn’t the problem, though; the problem is working out why other Pokéballs don’t have the same effect on happiness – because presumably Ultra Balls work more effectively because they are more comfortable, all around, than Pokéballs, and Lure Balls are more comfortable for Water Pokémon specifically, and so on; they do the same thing as we imagine a Luxury Ball to be doing, only much faster since it’s all pre-set.  Maybe we could imagine that having a lesser effect on happiness, since the Pokéball isn’t ‘tailored’ (as it were) for the Pokémon, but surely it would still have some?

Of course, we could always revert to what would seem to be the default explanation, which is that Ultra Balls and the like introduce some element of compulsion into the whole business.  That does make perfect sense in itself; it’s more of a ‘is this the kind of theme we want our fiction to be portraying?’ question.