Blood, sweat, and tears!
Seriously, when you nest containers inside of containers (or any object), there will be default margin and padding applied. You’ll need to counter that with CSS for web apps to get the alignment that you are looking for. Alternatively, don’t use tables and just drop the objects in the container and use CSS to place them how you want. That requires a different skill set than just using Mendix off the shelf, so the last suggestion I’ll make is to mess around with putting and removing containers of the different sections to get them to align better. But really, custom CSS is the only way I know of to make it be “perfect”.