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For example I'm fighting this Alpha Luxio, and if the catch rates don't change, it shouldn't be that hard to catch with a PokeBall.

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I’m pretty sure this was confirmed via plot


Basically, yes
Anecdotally I'd say yes as well. I tried to catch the alphas from the Sea Legend quest but they kept breaking out.
What Alphas in the Sea's Legend quest? Isn't that the Manaphy one?
Yeah, there aren't any alphas in the sea legends quest

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Not only are these intimidating variants markedly bigger, stronger, and more aggressive than their standard counterparts, but they're significantly more difficult to catch as well.

Source

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"they're significantly more difficult to catch as well" could very well refer to the fact that they're much higher level than a player's pokémon, since most players aren't used to facing such high level opponents. I don't see anything written about catch rates in the article, so are you sure that that one line is sufficient to answer (and that extremely random gaming website in general, since most of them have a mixed reputation)?
The source is fine, and it (what the question asks) is a fact which is taken for granted in PL:A discussion servers/subreddits.