How do I run multiple syncthing processes on the same machine?

Given the usage scenario, the least complex method would be to configure a single instance of Syncthing in your Ubuntu VM with a consistent Syncthing folder naming scheme for every incoming folder.

One of the things I would recommend doing differently from the tutorial you mentioned, is to use a systemd user service instead of a system service.

Please see the following earlier posts where I describe a single instance setup for multiple users and using a systemd user service instead of a system service: