That should not happen if the instructions were followed properly. They don’t add the PlatformIO python to the $PATH, only a symbolic link to the pio executables are created in ~/.local/bin.
In a regular terminal:
max@max-VirtualBox:~$ pip3 -V
pip 22.0.2 from /usr/lib/python3/dist-packages/pip (python 3.10)
max@max-VirtualBox:~$ pip -V
pip 20.3.4 from /usr/local/lib/python2.7/dist-packages/pip (python 2.7)
max@max-VirtualBox:~$ which pip
/usr/local/bin/pip
max@max-VirtualBox:~$ which python3
/usr/bin/python3
max@max-VirtualBox:~$ which pio
/home/max/.local/bin/pio
max@max-VirtualBox:~$ pio --version
PlatformIO Core, version 6.1.5
max@max-VirtualBox:~$ echo $PATH
/home/max/.local/bin:/home/max/Downloads/cross-pi-gcc-10.2.0-0/bin/:/home/max/.local/bin:/home/max/.local/bin:/home/max/.cargo/bin:/home/max/Downloads/cross-pi-gcc-10.2.0-0/bin/:/home/max/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/snap/bin
Double check that ~/.platformio... is not in your $PATH, remove it if needed from ~/.profile / ~/.bash_profile and perform the installation steps exactly as in the guide.
Note: It is expected that when you use VSCode and the “PlatformIO Core CLI”, that this opens inside the PlatformIO environment.
max@max-VirtualBox:~/x16-demo$ pip -V
pip 22.3.1 from /home/max/.platformio/penv/lib/python3.10/site-packages/pip (python 3.10)