Trying to apply any sort of realism test to any of the games warfare subsystem will just end up leaving you all aggravated and confused. Its not a military simulation by any stretch.
Elements of the warfare subsystem are loosely tied to real-world analogs, but they dont simulate anything. In the case of the change in use of enemy roads in Civ 3, it makes sense all around. Its an excellent game-balancing tool that prevents those tank rush one-turn conquests of vast empires. It is also a stronger analog to the real world than the Civ 2 treatment.
In the real world, large military formations dont go dashing down enemy-held road networks in column of march because thats a good way to get shot to bits. Lots of times they dont go dashing down those same roads for even simpler reasons: They have crummy maps, bad navigation and even worse driving.
Civ 3 slows the use of enemy roads to force military campaigns into a more historical model and to balance the game. I thought the ability to fly around the map in Civ 2 like a cannon-armed ping-pong ball was one of the games dopier aspects.
Dralix:
You can still chain-gang a railway through newly-conquered territory in one turn. You just need a pile of workers (or slave workers, more typically) to do it. Depending on your government type, you need like three or four slave workers to pop a railroad down in the same turn. Then you move four more workers through those to the next road tile and repeat the process.
In fact, the territory can belong to a technologically backwards Ally as well. In the last game I played (as the Aztecs), the Germans started a war with me after they had plopped down a city in an empty spot (emptied by a previous war that caused me to raze a city that had been there) that cut off the northern five cities of my empire. There was also a route to those cities through Zulu territory. The Zulus werent laying rails yet, so I struck an MPP with the Zulu and chain-ganged a railway through their territory in one turn to rush reinforcements north. It helped, of course, that I had about sixty slave workers hanging around from previous wars.
The Germans were not happy about this. But none of them were left to complain a few turns later.
Cheers.