If you have chosen the system-wide installation of the nRF Connect SDK on macOS and Linux, add your environment variables in ~/.bashrc, for example the GNUARMEMB_TOOLCHAIN_PATH variable. Unfortunately, VS Code does not pick up environment variables added to this file, even when launching VS Code from a terminal.
To get around this issue, the extension queries Bash for its environment on Linux and macOS. This executes the ~/.bashrc file, as well as any other files that run when starting Bash. If any of these files execute behavior that you do not want, either check for $NRF_CONNECT_VSCODE in your Bash scripts or change the nrf-connect.west.env setting.