not 100% sure if I understood your question correct. I am always using Container to divide my page in Sections, e.g. Navbar, Hero, Section1, Section2 etc. These sections usually then have a padding on the top and bottom of mostly 12 or 16 pixels to give the design then some space to breath.
When I am using then anchors in the navigation I jump always to the Section (and not to a header or so). That was in my cases always perfect.
