@EricAnderson the mention of highly recommended as an application was from me for a previous era of MAS and Windows Servers. In my own experiences, since Server 2008 R2 and higher and with MAS 4.50+, I've had several good experiences with running the App Server as a service so long as it's running with an appropriate domain account and the heap size settings in the registry are set appropriately for the service.
I'm also very familiar with the Microsoft Autologon utility (originally a Sysinternals utility from Mark Russinovich) which can accomplish the desktop app login -
http://technet.microsoft.com/en-us/sysinternals/bb963905 - it would be easier to push this to IT. I'm not familiar with FireDaemon. In the end since the server needs to get rebooted nightly, my take is either Autologon or run as a service