The system-property=* resources represent user-provided configuration that was read from and will be persisted to the standalone/domain/host.xml config files. It's not the complete set of system properties. So when you do the :add operation you adding persistent configuration, not just changing the value of the property in the running VM.
If you want to modify a property that already exists in the VM but wasn't part of the persistent configuration, use the :add operation as described above.
I recognize this isn't exactly intuitive.