They go together; Bootstrap 4 will have an option to use flexboxes to implement its grid system.

It's an option and not the default because there are a lot of browsers out there that don't support flexboxes yet; give it a few years and this will be a much more practical choice.

That's like asking about the advantage of driving a stick shift over a Mercedes Benz.

It's meant to be used alongside the grid system of bootstrap/foundation/pure/etc... As a rule of thumb: grid system for the general positioning in the page, flexbox to align the items of the block.