i think you need to look into routing. Specifically, split tunneling.
https://tailscale.com/learn/what-is-split-tunneling-secure-critical-data-vpn
https://protonvpn.com/support/protonvpn-split-tunneling
https://mullvad.net/en/help/split-tunneling-with-the-mullvad-app
I’d recommend installing those python dependencies using apt, so that when you update your system packages, the python libraries get updated, too. Pip, on the other hand, is useful for development but is detatched from apt and you will definitely forget to pip update unlike apt update which you hopefully do frequently. Use the names of the packages the readme provides in the pip install … instruction. For example, for numpy, you can install this.
Then, since that python script has a shebang at the top, you can add it to a directory in your $PATH and mark it executable with chmod, and you can invoke the script in your shell from any directory with just the file name.
from a design perspective, consistency is key. light mode is on? then light mode means light mode, and apps should be in light mode.
do you want both your terminal to be dark theme and your gtk apps (including all of the gnome UI) to be light theme at the same time?
do you want settings within every single app in order to change from light mode to dark mode, as opposed to a global toggle that applies to every UI on your computer?
alternatively, is the terminal the only exception to this global toggle, and this design inconsistency by having the default contradict the default of the rest of your desktop environment is your preference?