A quick glance at the source, and a read of your email, suggests that the only reason you'd see the logging is if people were using the extension. The Right Thing to do is not to install the old extension if we're using geckodriver. I _think_ the Java bindings do this now, but I'd need to check properly. Obviously, blindly installing the legacy extension is less than efficient :)
Although the official line for Firefox support is N, N-1, ESR, ESR-1, I really do think we need to make an exception for the legacy firefox driver. There are already enough people who haven't upgraded their selenium versions because they believe that doing so would prevent them from using the old driver. Having said that, I also think that when we ship 4.0, that support should be in a legacy jar of some kind, and I'm okay with that only being available through the selenium server. (That is, we hurt our users by deleting the old driver. I'm not a fan of doing that)
Even if we do move it to a separate jar, the code will still be in master. Let's figure out where this setting is being injected, and then tweak that if we detect we're using geckodriver.