J. Koch wrote:
1. Which run configuration gets applied when you start a JBoss AS remotely over SSH from local JBoss Tools?
JBoss Tools server adapter doesn't use any .config file form bin folder, it just generates VM parameters in LocalJBoss71ServerRuntime.getDefaultRunVMArgs(IPath serverHome) and then run server with java using those parameters on local or remote host. Parameters can be changed through editing launch configuration for server.
J. Koch wrote:
2. Is there a secured way to debug the remote server, like over SSH or HTTPS or at least protected by username and password?
There is an article Remote Java Debugging via SSH Tunnel Only Works if Local and Remote Ports are Identical. It could help, considering you added missing parameters to command used to start serer on remote host (note, I'm just guessing and haven't tried that myself).