This is a neat idea. I think for this to work mid-to-late game, there needs to be some mobile means of constructing separate logistic networks.

I propose a new train car that is a self contained roboport. Bots are locked to it, and don't travel to other roboports. The only way to add / remove bots is the normal method for loading and unloading a train car.

You can construct separate logistic networks even today (bots can build a roboport that isn't connected to any existing logistic networks, or you can remove roboport to split logistic networks).

Unfortunately it's not easy (nor possible, I think) to add new entities in a scenario. I'd have to add them in the "mod" which would make them available for all games, not just BNW scenarios. I'd rather not do this because I want this mod to be a pure scenario mod, so you don't have to enable/disable it all the time; any non-BNW games won't be affected at all if the BNW "mod" is enabled.

However, there may be a solution for you:
Search for "vehicle grid" mods. Such mods add equipment grids to vehicles, so you can place a portable roboport in vehicles. Although, I'm not sure if these will actually work if you place conbots in wagons, I've never tested.
Another possibility is FARL, although again I've not tested if this actually works.

Optera's Vehicle Grids + Personal Roboport. There is also a logistic cargo wagon mod that might help.