It is actualy really simple if you can change webserver config. I have this rule in site config (nginx):
location ~ /\.well-known/acme-challenge/ { proxy_pass http://letsencrypt.example.org:8081; }
Letsencrypt is running on machine http://letsencrypt.example.org1 with port mapped from 8081 to 80.
I can now simply verify domain running on different machines with single instance.