(Best) approach to sync multiple programs under single root to GitHub?

I have this repository that I currently work on with the Arduino IDE but would also like to maintain it with VSCode/PlatformIO:

So I have two different code files (DuploTrainControl.ino and PS3LegoinoControl.ino) each in their respectively named subdirectories (which is a requirement for people who want to compile under Arduino IDE). In the root directory, I have the general README.md.
Both scripts run under the same platform (ESP32), but will have to be flashed on two different ESP32 microcontrollers for the project as a whole to work (similar to a client-server approach).

What I want to achieve are two things:

  1. I want to be able to compile both files independently. This could work if src_dir was not a platformio.ini-wide configuration, but could be set based on the environment sections, but this is not possible, apparently. Using a multi-root/multi-project workspace could work but would create two different directory structures with each project having its own src, libs etc. directories which seems to make it impossible that I can…
  2. Sync the current directory structure back and forth from/to GitHub. When using multi-root/muti-project workspaces, I will have all the added directories that platformio needs and thus the root directory which contains the README.md etc. will no longer be a direct parent of the two code-directories.

What would be the best approach to achieve these two goals? With the ArduinoIDE this is not a problem, but I don’t want to go back there after having tasted VSCode/PlatformIO :)… Any help is highly appreciated!