For the older scissor keys, you can get replacement keycaps from ebay, and install them with a bit of fidgeting yourself. So even if Apple doesn't replace individual keys, you can do it yourself, and fix a broken keyboard for around 15€.
With the new butterfly keys that is apparently no longer possible.
Apple and Apple service providers can get replacement keycaps from Apple and replace keycaps, even for the butterfly keyboards. The linked article even says, "The type of service [...] may involve the replacement of one or more keys". The butterfly ones are more complicated to replace.
But this only helps with some kinds of key issues where the keycap or scissor mechanism is the problem, like sticking or rubbing keys (and dirty keys). It usually doesn't help with issues like no key response or wrong letter being typed. In this case the keyboard, and therefore the top case, would need to be replaced.
A few years ago I brought a 2011 Macbook Air to an Apple authorized repair shop, and they told me they could only replace the entire keyboard. So if they started replacing individual keys, that must be something new, I've never heard about that.
Everything I've read suggests that they only replace the entire keyboard, or in the case of the new Macbook, the entire top half of the computer.
I've also read that the scissor switch breaks when you try to remove the keycap, so I'm not sure how replacing individual keys would work.
I've replaced many Mac keycaps. All the "chicklet" style, starting with the white plastic MacBooks, can be replaced. (I don't know about the silver MBPs keys before that.) I honestly don't remember when key cap sets became available. Possibly after the retina MBPs came out, which use the same keycaps as the Airs. With the white MacBooks, with their infamous palmrest cracking issue, there were always extra top cases around to take a key from. This is still what is usually offered, at no cost, to someone who needs a key or a few, if they're off warranty.
The big thing is the keycaps and scissor aren't designed to be removed, unlike other parts of the machine, so you will break a large fraction of the ones you try to remove, and those will need to be replaced with a new key and/or scissor. And they're small and fiddly to replace. So there's a difference between replacing 1, 2 or 3 missing or wonky keys and half the keyboard. Many shops would probably only want to replace the whole top case after a certain threshold due to the time and work involved. If the keys are sticky it's different too, since the keycap, scissor plus the part of the top case below and around the key would need to be cleaned to get it moving well. With more than a few keys this starts to be a lot of work.
The butterfly keyboards don't have replaceable mechanisms, and the keycap's tabs are so small that they are not meant to be put back on, but instead always replaced.
OK, this sounds reasonable. In my case, there was a single broken key on the keyboard (either the cap or the scissor was broken, I ended up replacing both with a used key from ebay), and the Apple authorized service provider told me they could only replace the whole keyboard. Good to hear that this is not an actual Apple policy, because it seems ridiculous.
With the new butterfly keys that is apparently no longer possible.