If both compilers are correct, which compiler you compiled the program (compiler in this case) with shouldn't matter for the correctness of the code; but the generated code would be different. There should be no difference in the code generated by instances of the same compiler version, although the code of the compiler programs itself would be different (i.e. different performance, time of exec...) if they were compiled with different compiler versions.

Edit: That's all assuming same version of the language being compiled. That's why they say the go1.x compilers may need to stay restricted to go 1.4 for their code.

P.S. See Linux From Scratch or osdev.org for more about this