If:
1) your market is fragmented
2) many clients are cheap phones that don't support AES-NI
3) you can differentiate them so that you don't penalize better clients
Then yeah it makes sense to use Chacha20-Poly1305 for some of these clients.
But choosing Chacha20-Poly1305 over AES-GCM all the time doesn't, and I'm not sure why Wireguard does that (besides trying to be trendy).