Some thoughts, not ordered.
We have strong indications that dark matter and dark energy exist, they influence normal matter at least by gravitation hence have an effect on zero K internal energy but are not known in their nature nor full effects. And what if we discover a fifth force?
From time to time we discover a huge mass in our galactic supercluster (Relativity is very concrete here: because we fall freely, it's difficult to detect the effect). How should we know if we included all masses?
The nearby supernova 1987A changed the gravitational potential in our vicinity by 4.7mJ/kg (wow!) which we didn't notice at all (I speculate Lisa would have). If we don't notice such changes, I feel reasonable to live with relative energies.
I'm interested by thermo data at 298K 1atm, not at zero K. The transition between them is generally undocumented or inaccurate. I'm happy that people sometimes produce true measures converted to standard conditions, not to the zero K I can't use.
Rotations, vibrations and so on are vaguely estimated by software. Enthalpies of formation by software are far too inaccurate, even at zero K. Building a data system on that would be of no value to me.
Some weird effects exist at molecules' rotation and zero-point energy, for instance ortho- and para-hydrogen. I'm not sure that software can predict more complicated molecules properly.
No, we can't estimate the internal energy, because we have no means to compute a melting point nor a fusion enthalpy. This fails up to now, consistently and the big way, typically by 50K. So the internal energy of a solid at zero K is not predictable presently.
I doubt we can estimate the electron energy of heavy elements, and certainly not with the accuracy wanted by thermochemistry. 1kJ/mol is only 10meV. Better put the zero reference energy at a complete neutral atom than at separate electrons, protons, neutrons.
"You could calculate nuclear binding energies", I doubt that one. Existing models are primitive and typically explain the general shape of the mass default curve. These days, experimenters discover things like "beryllium contains two alphas far from an other plus a diffuse neutron", or "we find more often a neutron close to a proton" and theory had predicted none of them. How could it have predicted the mass of the nuclides? Though, we're speaking of many eV error here, nothing that chemists want to accept in thermo calculations. Chemists better take an arbitrary reference that ignores nuclear forces, that is, complete atoms.
If willing to exaggerate further, protons and neutrons are composite particles, so we should compute energies starting from quarks and gluons. Worry: nobody can do it accurately now. The mass of lone protons and neutrons is known, but not of lone quarks since these do not exist, nor is their interaction energy known. So protons and neutrons are obviously less bad a zero reference than quarks and gluons.
And anyway, we ignore which particles are elementary. Where shall we stop?
Our mere incapacity to tell if we know all forces and if particles are elementary is a hint that energy is not absolute. If departure from some absolute reference were measurable, we could tell all that.