I personally am a fan of remove as much old as possible when doing mods or upgrades though.

If it was me I'd keep the transformer then. It's definitely worth it for ease of life. There's no real drawback to keeping it but you can rest reasonably assured you wont have power issues since the last car ran with that setup without issues. I wouldn't want to cause any power issues in the building backfeeding harmonics and possibly interfere with other items in the building. And if there was more than one car I'd definitely want isolation in some form to prevent dirty power between cars messing with the drives or other parts of the controller.

That is odd. Most every traction controller I work on with a vvvf drive has a line reactor. I wonder why alphas not using one. Kind of one of those extra steps for top quality you take in advance to prevent problems instead of waiting to see if you have problems. I would at least want some ferrite rings on the power wires going into the drive.