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.
I had a similar issue with the anchor section appearing behind the Sticky menu. the solution was to add the following into the advanced section of the container of your anchor. Adjust the number of px accordingly as needed.