Right now for active check to work Host "Host name" field should match with zabbix_agent.conf HostName of HostNameItem.
Host "Host name" field must be unique. And zabbix_agent.conf HostName of HostNameItem cannot accept multiple values.

So, if we use Host prototypes, which "Host name" fields also must be unique there is absolutely no way we can use Zabbix agent active checks with Host prototypes because HostName in zabbix_agent.conf will never match any LLD dicovered Hosts "Host name" field.

I would propose that there should be additional field in Zabbix agent active check configuration which explicitly specifies to which Host "Host name" this item is linked. And it should be possible to be set to "LLD parent Host" during LLD.
So Zabbix agent would receive additional list of active checks for its HostName with some ID to pass through back with data to put associate it with corret item from discovered Host.

Idea here is to remove unnecesary load in Zabbix server/proxy poller processes and thus bottlenecks and move from pull to push interaction.