Hi,
my comment wasn't about adding WP-CLI per se. I don't really mind at all since installing it is just a matter of a few seconds (copy/pasting 3-4 commands). I just mentioned it as an easy and safe way for Webinoly to modify options on a WP installation. If Webinoly installs a few plugins, it would make sense taking care of their appropriate settings as well.
In general, I am not against the approach that you describe. In fact, I would prefer to have an option to an ever more lightweight installation, with phpMyAdmin, backup tools and datahog being optional addons (I don't use phpMyAdmin at all so I remove it right away and I use backupPC for the server updates, so I don't need the backup functionality either). I would, however, like the idea of having the option to add such functionality in the form of extra "addons", with support for tools that can be challenging to setup correctly, like Monit, fail2ban etc. But that's an entirely different discussion I guess.
Returning to the discussion about the two plugins, you mentioned that their use is optional. Does it mean that I could remove them while having -cache=on and my site would keep working as expected? What I thought that they do was that they make sure that the cache gets purged everytime a post or page gets modified and that without them I would have to manually purge it from command-line. Is this true or am I completely misunderstanding it?