Domain reflects jboss.server.xy properties, tested with jboss.server.log.dir property.
The same server.log file is used for both server-one and server-two. Only file boot.log is created in domain/servers/server-one/log and domain/servers/server-two/log directory. In my case file server.log contains log only for server-one, there is no log for server-two.
I think jboss.server.xy properties shouldn't be reflected in domain instances.
Even structure of https://docs.jboss.org/author/display/AS71/Command+line+parameters implies that jboss.server.xy properties are used for Standalone.
Reproducer of my steps: