In short: It depends.
Widget go into a widget area. But that also means that when you create a widget area any widget can be put there as well as any number of widgets. So if you’d make the logo a widget a user could put twenty different widgets in that spot, including stuff that doesn’t really make sense there and could break the layout. So generally speaking widgets are only well suited for generic content regions like e.g. sidebars.
When using the Customizer you have more control and can create a UI that defines clearer what is doable. For example you can let the user choose an image, but he can’t put e.g. a tag cloud widget there instead.
As a final note this whole question also has a historic aspect: Widgets have been in WP for a long time, the Customizer was only later created, partly to overcome the limitations widgets have.