I currently have a single HA instance, running as a hassio installation on a linux VM as per the installation instructions. The VM hostname is docker3.domain.net but HA is accessed as hassio.local or hassio..net.
I now want to add a second HA instance running on a Pi3B+.
By default, this too will register itself as hassio.local and hassio..net.
Do I have to change the hostname of the new instance, and if so, how?
I have two instances of Hassio. A main system and a backup system to be used in case of hardware failure of the main. Normally this backup is powered down but if I do power it up while the main system is running I can access both of them perfectly fine via their IP address.
Indeed you can, however you can’t access them both via a domain name. As every other device in the network is accessed via a name, I am loath to having to reduce functionality: mainly because of the hassle if the underlying WiFi adapter is changed.