So why not breed humans in cages for experimental research? Then they'd just be "material with a specific function" as well. Same argument. If we discovered tomorrow that humanity was actually a breeding colony created by alien researchers would that somehow reduce the value of your life to you?
Because we agree that this would be cruel, "do unto others what you wish done unto you", "we can do better than that", etc. We think it abhorrent to regard other people as material.
But to be perfectly honest, I don't see the life of a bird anywhere near equivalent to the life of a human, i.e. even though birds have intelligence >0 and show feelings in form of caring towards their young, the classical "you can only save one" scenario would be no real contest IMO. Is it "speciesism"? Where does it stop? Can it justify racism? (the last question is an easy "no", but not on topic here)
Or can we say that our species is a priority, but the life of a dog is worth X hours of a homo sapiens suffering at a specified intensity... and then "trade" in this norm.
Now that would be an interesting though unnatural concept. We only "recently" started with the novelty of caring at all for other species, where it benefits us (cattle, guard dogs, pretty view in a zoo), so the main problem would be finding the sweet spot.
With regards to other species, we usually practise right of strength, with constraints (like the eschewal of unnecessary cruelty) that are actually much more about ourselves.
As for us being bred by aliens: the question is more like "Why should they keep enabling our ability to reproduce / the sun burning / ... and does this give them the right to do certain things with our offspring, within limits only they decide upon and we can't influence?" ... full of helpless, doomed, cold irony, that one.
As for your second paragraph you leave a gaping ethical hole: what of the intelligent beings created illegally? We're probably not far from the point of being able to manipulate organisms to develop human-class sapience - if the only protection such creatures have is that it's illegal to create them in the first place then what happens to them when they are discovered? By any ethical yardstick they would be people, but people with no claim to human rights. Do we just say "Hey, a slave race, cool. We created you so we can do whatever we like. But don't worry, we threw your creators in prison so it's all good."?
A big part of this question is technical. If they were created illegally, the perpetrators should be punished and prevented from doing so again, and measures should be taken so this doesn't happen. What to do with them after the fact is an open question. Assuming that they are somewhat equivalent to humans, why not give them full membership of humanity and be done with it? This would be roughly in line with female suffrage, non-white-male-land-owner rights and similar achievements. If they are illegal to create, immediately set free upon discovery and their creators punished, there would be not much of a motive to create them. What their creators do with them in secret is a moot point, just as with those guys who hold their daughters or other women captive for years and rape them (Fritzl et al).
Now if a democratic majority actually said "Yay, cheap slave species!" ... well, we've had that many times already, so there's hope we'll overcome it with regards to highly intelligent artificial beings just like we did with other races/tribes.
The more tricky part is what to do with beings that are not equivalent to humans, or of highly debatable equivalence. Like chimps. And if that is resolved favourably for chimps, then orang utans, dolphins, dogs, and so on.
I do not contest that the gains of animal experimentation may well be worth the sacrifice, my objection is only that the ones making the sacrifice are given no choice in the matter, and the people performing the experiments tend to deny that the moral dilemma exists at all. Perfectly understandable from a perspective of their own psychological well-being, but intellectually dishonest. And it means it has to fall on the rest of us what sort of moral price we're willing to pay
The devils advocate says that there is no moral dillemma if we're talking about "material with a specific function", even "material" with cognitive capabilities.
And in practice, this is precisely what we're creating. I've already asked whether this should be allowed in my previous comment... IMO within limits that are important for us and our ethics, not those of the animals, since we can't ask our creations about such things (yet).