I don't see what having multiple transports on a navigation route buys you. The transport is an abstract thing. It's a flag that is either true or false. It means either you can use the navigation route or you can't. In no way does it affect how many units can use the navigation route.
The offensive module requires you to destroy a transport. If you were able to build multiple transports, you could utilise these to make multiple attacks on the enemy base without needing a build order between.