It makes no difference (from what I know) if you use deployment-scanner or CLI.
The problem is more the naming conflict.
If you have the same ear/war binary and deploy it with different names you can reach the application with different names.
If you have the same context-root for your webapp it will fail.
If you deploy a app with CLI and the same app is droped to deployment directory earlier you need to use --force to overwrite. In that case the CLI deployed app will win, also if you restart later.
I recommend to not use such approach in production, I often remove hotdeployment (the complete deployment-scanner in AS7) to ensure that the deployment is not done by touching files.
I don't know that this is true, as we have seen some peculiar behavior such as one user uploading a war via ssh direclty to the /deployments/ directory to replace the one that was loaded in the console and the user still sees the content from the war loaded by the console. I need to do some experimenting with this when I have time.
I've checked that local with a current EAP6.1.
It might be that you have changed the scanner configuration.
But as for such remote access I recommend to use the CLI as I'm not sure whether all remote copy commands are atomic. It might happen that you will have unwanted results.