Andrew Mason said:
But the three spatial dimensions are arbitrary (so long as they are mutually orthogonal) whereas the time dimension is not.
The time dimension is orthogonal to the three spatial dimensions. By scaling them you form an orthonormal set of basis vectors. To do that each of the four basis vectors must be mutually orthogonal unit vectors.
In an inertial reference frame one can describe the space time coordinates of an event relative to the origin as (ct, x, y, z) where x, y and z can be anything so long as x2+y2+z2 is always the same. But you cannot do that with t.
That's what he means about the metric being different. It's not ##x^2+y^2+z^2##, it's ##(ct)^2-x^2-y^2-z^2## (timelike). As a result of the metric being different you can still exchange x, y, and z with each other, but you cannot exchange ct with x, y, or z.
None of that has anything to do with making the basis vectors orthonormal.
I will agree that speaking about mass as a form of potential energy is out of vogue. But there is nothing intrinsically wrong with saying that rest energy is a form of potential energy. The only way a particle's rest energy can be completely released is through annihilation with its anti-particle, and those are generally in short supply in our neck of the universe, so it is not really practical to treat rest energy as potential energy. But even Einstein in his 1907 essay on relativity spoke about rest energy as potential energy.
In the example you gave of an atom absorbing a photon look at the total energy of the system in its center of momentum frame before the absorption. In the low speed approximation it's ##h \nu + Mc^2##; after the absorption it's ##(M+m)c^2##, where ##M## is the mass of the atom before absorption and ##(M+m)## is the mass afterwards. (I think the approximation I'm using may also require that ##Mc^2>>h \nu##, but either way it's satisfied!) The contribution to the rest energy made by the photon is ##h \nu##, and it's equal to ##mc^2##.
If you divide each term by ##c^2## you get the mass. That is, the mass of the system before the absorption is ##h \nu/c^2 + M## and afterwards it's ##(M+m)##. The contribution to the mass made by the photon is ##h \nu/c^2##, and it's equal to ##m##.
So what is being converted here? The thing called the energy contribution, ##h \nu##, is being converted into the thing called the mass contribution ##m##, or is the thing called the mass contribution ##h \nu/c^2## being converted into the energy contribution ##mc^2##? Now, this is all semantics of course. Rest energy and mass are two names for the same thing. The total mass of the system before the absorption equals the total mass afterwards. And the total rest energy of the system before the absorption equals the total rest energy afterwards.
The pedagogical point being made here is that the factor of ##c^2## is considered by some to obscure the physics. But regardless of anyone's opinion on that matter, rest energy and mass are equivalent. Note that to see the equivalence you must look at composite bodies, that is, systems that consist of entities.
Also note that you can do the same thing with energy and momentum vector components that you can with time and space vector components, respectively. When you do that the factor of ##c## gets in the way because, and I hope I'm saying this right, the basis vectors aren't orthonormal.