I could say, "does it matter? they all work under the same programming". I now have two aircraft with this idiocy, and apparently it is an issue that's plagued FS2004 at least 20 years ...I've found threads that old complaining of it ...with no "one size fits all" solution.
The Travelair 4000 comes with full electrical system, and the default instructions for starting - master switch on, fuel valve open, magneto to "both", hit the starter, engine turns a few seconds and fires up. Or you can leave all switches and valves off, hit CNTRL+E, and all switches pop to their proper positions and the engine starts.
The SimTech Dr1 has no default electrical system, just hit CNTRL+E when necessary (if the throttle is below around 50% there's a chance of the engine stalling ...most landings involve killing the engine once over the runway and gliding down). I added a master switch, starter, and fuel valve (there's a magneto in the VC).
I cannot manually start either plane - all switches/valves properly set, hit the starter and rrrr-rrrr-rrrr-rrrr (doubly annoying in the DR1 since it has no brakes, the prop spinning at starting speed is enough to get it rolling around the runway). On the other hand, either will start almost instantly from CNTRL+E. The system is recognizing the controls since the switches in both planes will go to their proper positions during a CNTRL+E start, and closing the fuel valves will kill the engines. As someone in one of those old posts pointed out, CNTRL+E must be doing something besides just operating the switches and valves ...but what?