For molecular orbitals, how is an energy of zero set or defined? When labeling the energies of molecular orbitals, often some anti-bonding MOs are shown with a positive energy. For example, MolCalc has the following energies for methane (the anti-bonding MO #8 at +19.47 eV depicted on the right):



I'm trying to understand what these numbers mean. I get that electrons in MOs #2 through #5 help to keep atoms bound (having them occupied contributes to bonding), whereas electrons in MOs #6 through #9 would lead to an increase in bond lengths or the molecule falling apart. On the other hand, MO #1 does not participate in bonding, right (basically, it is the inner 1s electrons of carbon)?

So what defines the zero reference point of these orbitals? It can't be the free electron because I thought at least for the hydrogen atom, even the excited states are states where the electron is still bound (i.e. energies are negative). It can't be the gradient of increasing all bond lengths (i.e. with the extreme case being separate atoms) because MO #1 would be hardly affected by that, given that it hardly participates in bonding.

This question is not limited to one particular software or author. Here is another example (source: https://www.researchgate.net/publication/234126374_Electron_rectification_through_donor-acceptor-heterocyclics_connected_to_cumulenic_bridge_A_computational_study):



I realize that the language in this question is sloppy, reflecting my poor understanding. I encourage anyone who answers to use the correct terminology.
The answer technically depends on the method. In most cases, meaning HF or DFT with standard basis sets, it is infinite separation of all bare nuclei and all electrons. One exception known to me is VASP (a periodic, solid-state code), which uses pseudopotentials to avoid having to model the core singularity and core electrons. There, the zero-point is in reference to some atomic state.

Note that the MO energies are basis-set dependent, which is most pronounced and most easily understood for core electrons.