As many panels do not have an avionics, and battery switch it would be hard to spin up from absolute cold, this is my tactic:
- Start FS, create the flight, and start it.
- Ask for clearence (offline ATC of course) and shut down the engines.
- Start Logger and setup it
- Do your preflight preparations, and startup engines only after that.
This way you will not get penalties. Before you start the Logger you can start FSPassengers for example and let the pax boarding, while you setup the airplane for the flight.