I've done a little messing around and written a script to start flightgear as I wish
https://github.com/jonititan/FlightGear-Customisations/blob/master/CommandLineStart.py
However I currently haven't found a way to use the autostart feature from the command line.
My backup plan is to just step through the checklist after startup using telnet as I'm not really interested in flying personally but just starting the sim in arbitrary situations and then writing AI to use with it.
I've been over the wiki and the Nasal stuff but can't currently see anything obvious regarding calling the the autostart function from systems.nas
Thanks in advance for any help.