Our customer wants to use an SQL Server Cluster with dynamic ports, and so far, I have found the following solution:
Install from ZIP
1) Replace jtds-1.2.4.jar with jtds-1.3.jar (possibly the one from http://sourceforge.net/p/jtds/discussion/104389/thread/20f728dd/ until 1.3.1 is available).
2) Select internal database for now.
3) At step 2, stop the service
4) Edit dbconfig.xml to not have a port number, and add ;instance=INSTANCE;domain=DOMAIN;user=USER;password=PASSWORD; to the connection string. Keep the normal user/password fields filled, as they are checked for existence and non-emptiness.
5) Start the service again, and continue with configuration.
This seems to work, and I would suggest that official support for 1.3.0, dynamic ports and Windows credentials might be a topic for work going forward, but I would like to know if this method will bring our customer in an unsupported state. As an argument to the contrary, I would like to point out that this is simply configuration parameters for an external component, namely jtds.
Note: This is our own SEN number as an Atlassian Partner, but the customer has already made the decision to buy a 500 user license that we just hasn't requested to be issued quite yet.