To nitpick, compilers nor linkers typically are not able to do "binary optimization", if by that you mean analyzing the asm and optimizing that. What happens when you compile with -flto or equivalent is that the compiler hides some internal representation in a special section in the object files, then at the link stage (if you also use -flto when linking) is that the linker invokes the compiler again which deserializes those trees from the object files, and does the inter-procedural optimizations on those.