AlextT two control panels should be tested

Alex, you stated that you can not test every control panel in use.  Yes, that is true.  However, two control panels are used quite often, Plesk and cPanel.  Therefore you could test those two to make sure that your instructions don't take down those panels.  I am sure Zarconia; as a Boonex partner, would be happy to set up two test sites using those control panel for you to test in the future.

# apt-get install nodejs npm mongodb-org graphicsmagick

Those are the instructions. They are Generic Ubuntu instructions. They work fine on a normal Ubuntu install. That Plesk has an issue with the 'npm' package is not a problem of BoonEx, or any of the hundreds of blogs or docs that have this same or a similar command. If there is anyone who should take action, it's Plesk for having a conflict issue with the default repo's NPM. I'm actually surprised it hasn't come up more often - maybe not a lot of people are running NodeJS on their Plesk servers with that version of Ubuntu.

The install doc at GitHub has already been updated with a note about the potential issue and to use the NodeSource repo to install NodeJS and NPM on Ubuntu servers running Plesk. I've also tested this a few times, and indeed, if Plesk is at the latest version (12.5) and this problem does happen, running the Plesk installer again fully restores Plesk with no issues. So as long as Plesk is up-to-date and if this does happen, it's recoverable.

I already tested on cPanel servers....  Works just fine.