Well, I figured it out (though I'm still uncertain why it was raccoons spawning, when it was cobblestone and not logs/shrubs). For anyone that had a similar problem, here's the gist; from what I gather, the night sky doesn't count as darkness because it's essentially a non-value (just empty space). So having your animals in a pen that lacks a ceiling is fine, so long as there's enough light inside the pen itself to keep them from de-spawning.
Of course, as shown in the pic provided, there was a ceiling over the pen that I made, and it's dark. Even though the pen itself is lit up, the game was counting the whole thing (pen and ceiling) as one space, and so the entirety of my barn was considered "dark" (we're talking almost losing my entire herd of gen 6 sheep to the darkness de-spawning mechanic type of "dark").
All that to say, the lovely vaulted ceilings I was planning simply weren't going to work. It would've been too much trouble and too many lanterns worth doing, so I ended up covering the whole thing over. No more raccoons have spawned since then, and neither have I lost anymore animals to the void of the dark ceiling.
I know this is all a very niche problem, but I spent hours scouring for an answer that I never found, and I'm sure I'm not the only one struggling with some of these more obscure issues, so I hope this is able to help anyone running into something similar (raccoons or otherwise)!
