I was also a little confused by their comment too, but I assumed they were imagining that the extension would cause the site to fail to load if the user started

I was also a little confused by their comment too, but I assumed they were imagining that the extension would cause the site to fail to load if the user started adding custom scripts into the page somehow. That doesn't mean that any data is sent to Facebook's servers telling them that the user tried to do this, but it would give Facebook confidence that only unmodified web apps are running. Of course, all this presupposes that the user has to install the extension to use WhatsApp on the web, which isn't the case. However, the extension could theoretically be made mandatory if it contained a load of obfuscated code that the web app was dependent on. That would basically mean implementing a type of DRM in the extension, and maybe there is some way to use EME to achieve that at a lower level. If a website ever started using techniques like that, then that would be the point at which to complain about disempowering users. Fortunately this plan doesn't do that, as you say, and merely allows users to optionally confirm that they are running the code they requested.