They don't quite say that this is a bad idea for use over WAN. If they intentionally avoided ruling out such usage in this qualification, they're making an implicit assumption here that either the last-mile connection or the endpoints themselves are going to be the bottleneck. If some router in between is having a bad day, it would definitely make its day worse.
edit: I wasn't familiar with Hysteria but now that I'm reading those docs, I guess the intent is for this to be used on the internet. In that case, it does seem pretty like it'd be pretty adversarial to run this. I bet if it saw widespread adoption it'd make ISPs pretty upset.
edit 2: Going slightly off-topic now, but I wonder if the bandwidth profile of Hysteria compromises its HTTP/3 masquerade?