There MIGHT be a byte that could be hex-edited in the "CFO_Weather.dll" file that would enable that, but I'm not sure (?).
That being said, I think that the reason that the time acceleration is locked to x4 (or lower) when the the autopilot is on is simply that the autopilot code in the game's engine can't handle anything higher.
As an example of this, I had previously fiddled around with missions and Quick Combat, along with higher-than-x4 time acceleration settings.
I *think* that the AI in the game flies their aircraft using similar code in the game as the autopilot. When I would set the time acceleration to anything higher than x4 (of course, without my autopilot on), the AI would have severe problems with flight (crashing into each other, into the ground, etc...).
*IF* the AI's flight code is similar to the player's autopilot code, then the above would be true... the autopilot simply can't handle anything higher than x4 without the aircraft being unstable.