Corpse stockpile:
Before visitors were introduced, the Corpse stockpile was reserved for dorfs, with everything else being sent to the Refuse stockpile, thus leading to caravans bolting as they approached the refuse stockpile, with dorfs suffering trauma, due to all the corpses of of sapients in the stockpile. That could be worked around by filtering the Corpse setting of the Refuse stockpiles on species, to get sapients into one stockpile and the rest into the regular one (you also had to deal with other Refuse stockpile sub categories, in particular teeth, as half a tooth was all it took for panic to set in.
Current implementation:
Corpses of all sapients are sent to the Corpse stockpile, and there is no sub settings, so troglodytes go there together with invaders and citizens. My suggestion was to allow you to send the "good" ones to one stockpile and the "trash" to another. Also note that corpses of undead of former sapients are treated as refuse, not Corpses.
It's true that only some creatures can be buried, and coffins check for that. However, it's rather difficult to bury the body of a defender when it's already been incinerated together with the bodies of the killed invaders (mine cart taking from the Corpse stockpile and dumping into magma, i.e. basically a quantum stockpile, but without the stocking and piling [I usually use a drawbridge at the bottom of a shaft to eliminate the corpses, but the effect is the same])...
Apart from the mechanics, I'd want those to be buried to be sent to a respectful morgue close to the burial grounds, while dead invaders are sent elsewhere and just disposed of using the method of your choice.
Sapient part crafting:
It's still possible, but you can't butcher the corpses. Instead, you have to have the corpses "butchered" naturally and let the arms/legs decay to release the bones that will then happily be used by dorfs for crafting (and if you don't monitor them they'll grab bones of undead of former sapients from the refuse stockpile if you happen to run out of bone elsewhere). It's even possible to use traps to do the "butchering", and with reanimation you can try repeatedly until the desired bits are severed. It's very inefficient, though, with most attempts failing.