Since I have some interesting ideas for deep recon missions and other creative uses of truly extravagant distances (with cutscene-based autopilot, of course), I decided to test the radius at which the desertion warnings will kick in.
I set out from the GTD Gayatea (no, that is not a typo) in a Horus, turned time compression up to 64x and engine power to maximum, and went out into the lonely void. I was smitten detonated by God Command about 600 kilometers out.
This leads to the question--why not make the radius 6,000 km? Or 60,000? Or 6.0 x 10100? Or not there at all? Or user defined? Having a hardcoded radius at which point you're blown up, despite the fact that objects can exist outside it, seems silly. Why not make the limits user defined, either as a definable radius (which can be eliminated by setting it to zero) or using a bounding box like asteroid fields, allowing a specific area to be carved out of space that is defined as the field of battle?
Besides, a single wing trekking out millions of kilometers in an enemy system to scout enemy movements is just really cool in ways that red-alert missions cannot possibly match.