Genuine question: does this mean that PieFed is now no longer ActivityPub compliant? Is it not fully part of the Threadiverse anymore, and is now its own little subset of that? Even Mbin still accepted vote counts, even though it added boosts (“increases” and “reductions” iirc?) on top of them.

Let's not catastrophise. Piefed is still ActivityPub compliant, or as compliant as it was. Nothing in the spec says you have to accept an activity, it'd be pretty nonsensical if it did because moderation wouldn't be possible.

Could you tell from your look at the code if PieFed is only throttling its own users internally, prior to votes federating out, or throttling incoming votes from Lemmy as well?

It's throttling incoming votes as well, you can see that here. It honestly wouldn't make much sense if it didn't, though it is irksome that it blocks announcing the vote to other instances. That makes piefed comms something the really active users will avoid.

Also this is so ridiculously easy to get around: most of us have a variety of obvious and self-acknowledged alts across the Threadiverse, but I doubt PieFed is going to maintain a mapping among all of them

Even if they tried to do that, people would just stop being forthcoming with their alts.