There is a way to workaround it but you need to maintain two servers. One for regular deployment with default servers settings and second with deployment to custom deploy folder which is in your case is something like "/path/to/your/jbossas/server/default/conf".

After you select "Make Deployable..." it shows dialog to select server to deploy so you can select second one with deployment to conf folder.

The only problem is that you have to publish it manually.