By default, the GNU compiler (gcc) optimizes each compilation unit (source file) separately. This is effective, but misses the opportunity to optimize across compilation units. Here is where the Link Time Optimization (LTO, option -flto) can help out: with a global view it can optimize one step further.
The other positive side effect is that the linker can flag possible issues like the one below which are not visible to the compiler alone:
type of '__SP_INIT' does not match original declaration [enabled by default]
Warning by LTO
MCU on Eclipse 