Another similar option would presumably be to delegate _acme-challenge.example.com to different nameservers with an NS record, then give your application the required privileges to control solely that nameserver.
Like so: Assume that Actor 1 has example.com and example.net. You then add this to the example.com and example.net zones, respectively:
_acme_challenge.example.com. CNAME example.com._.actor1._.your-special-domain.com.
_acme_challenge.example.net. CNAME example.net._.actor1._.your-special-domain.com.
Then you give update access to Actor 1, but not to the whole “your-special-domain.com” zone, but to the “_.actor1._.your-special-domain.com” subdomain. The ACME system would then be configured to send updates to the correct subdomains of that subdomain. Or “your-special-domain.com” could even be a subdomain itself of another domain; it doesn’t matter.