After overriding a theme's breakpoint definitions, trying to modify the media query values appears disabled when trying to update from the group admin page:

admin/config/media/breakpoints/groups/my_theme

However, after overriding the breakpoints, it is possible to update the values through the main admin page:

admin/config/media/breakpoints

It seems like a bug that the media queries can be modified through the main UI, but not the group specific UI.