In the Terminal, run the command:
env
In there you will likely see some PYTHON related variables. These variables are configuring how python behaves. You will also see the PATH variable which controls where it finds commands to run, ad in your case will include the path to python3.
In Keyboard Maestro, in the Preferences, Variables pane, set the corresponding ENV_ variables (eg ENV_PATH, and ENV_PYTHONLIB (or whatever the PYTHON variables are) to match your Terminal env results.