Since version v1.2.0 Toolbar Extras has a Smart Tweak setting to remove the regular “WordPress Widgets” from the Elementor Live Editor. By default this tweak is turned off, of course.
When working on a site with Elementor and you just don’t need those “old” WordPress Widgets that cannot be styled in Elementor then just deactivate them. That way you gain more space in Elementor’s panel and won’t get confused about the Widgets offered in the panel.
However, it would only make sense to activate this tweak if you definitely won’t use a WordPress Widget in Elementor content. Be aware that even some add-ons specifically made for Elementor use regular WordPress Widgets to add their stuff. An example for that is the (free) “Eleslider” add-on plugin.
Note: The “WordPress Widgets” category gets just hidden (unloaded), the Widgets itself are available in WordPress like before. The Widgets are NOT touched in any way, they only get no longer loaded and displayed within Elementor.