This seems to be a breaking change to me as well:
services.zigbee2mqtt.settings.homeassistant = true must be converted to services.zigbee2mqtt.settings.homeassistant.enabled = true.
Especially as the error message is not helping either:
error: evaluation aborted with the following error message: '(t.merge.v2 defs).value must only be accessed when
.headError == null. This is a bug in code that consumes a module system type.
As the default is set correctly this only happens when manually setting in the configuration (e.g. when home assistant is not running on the same server).