for me, position absolute and using top left or etc is troublesome, especially you will do the floating things between 2 div/section like my post here:
The never answered question
same does with margin and padding, you should know your own width and height divs, but it will too complicated when you turn into a responsive, you should set your width and height again.
the best thing to do responsive website i think you should follow the website structure. keep inside the wrap div or section.
in order to create the mobile view or responsive design you need the great media queries order, it help you to fit with a regular screen device like(iphone 5, 6 or ipad) but you have to consider that now market is in android. and android phone growing so fast and you can't learn what the resolution is(you won't update your media queries over time right?).
- bootstrap
it typeless but it only 12 grid system which you can't manage a navigation with 7 menu, you should modify it by yourself.
- flexbox
flexbox is good, you can maintain your container and you don't need to do using float and clear both.
like i said, it depends on your media queries. it's not about position or margin/padding, it's about everything in css.
if your question is only all about alignment, you can start using display flex with justify-content and align-items in parent div or section, this way you won't bother with what is your parent div's width and height.
cheers, might it help to understand :)