When we discuss the mass of a neutron and we say "one neutron weighs one u" then we discuss the mass of an electron and we say "one electron is 5.4858×10−4 u" and "one proton is 1.0072764 u" then we add them up and say "one hydrogen atom is 1.00794 u while one helium atom is 4.002602" (forgetting some complications for a moment) are we not just summing likes?

Or is it just that since mass is defined in Planck and time / distance terms that we need to relate it to counts of things? Theres a gap there I don't understand. Can we not just say "we measured a proton's mass and it is u"? Am I making a jump there?