The site says that "atoms" are an improvement over simple section interlacing. But I don't get how you are going to make this leap without changing the object file format. Linkers work on the section level because that is how object files work. Object files have sections, not atoms. Compilers emit sections as their basic, atomic unit of output. Within a section, the code will assume that all offsets referring to other parts of the section will be stable, so you can't chop a section apart without breaking the code.
How does the new linker work in terms of this new "atom" abstraction without changing the underlying object file format?