That only comes up the very, very first time, if the registry is completely empty of anything related to Scrivener 3 (same little starter setup as on Mac, only there is no keyboard section there, just the bit about setting up your backup folder and then offering to open the tutorial). Afterwards, you can switch presets via the Keyboard tab in Options, though, by clicking the down arrow button beside the Import button. This is how you would adopt the revised defaults if you wanted.
I do think F4 was changed as the base key for comments and footnotes, to avoid how close it is to Ctrl+F4 and Alt+F4, the latter two of which are hardly what anyone would want when going to insert a footnote and fumbling keys!
Changing the defaults on our end does nothing for those that already have the software installed, of course, so many will still have the old set unless they use the button mentioned above.