What about changing minimum distance to be between borders of factory, rather than from the single factory tile (maybe also add it to simuconf?)
I think it would be good enough if that value wasn't fixed but changeable in simuconf.tab (or so). Should be the easiest solution - pak64 players can leave it at 6 and pak128 players can change it to whatever they like.

Pretty much what I wanted to say! In fact I don't mind if its hard-coded into the engine, but increasing it to some value for pak128 would definitely help. Reading the largest factory size while reading paks on first starting the game and then fixing the minimum distance.
In 1 way I disagree to keep it customizable... It would increase the calculations when building factory chain and also by increasing it to a large value, it would mean easy profits for nothing. I actually like the fact that some factories around the city are so close that even though the finished goods is profitable, it doesn't have much to travel if its in the same city, thereby limiting your profits. (Though some reasonable distance is always desired, as is the subject)