Any user-accessible data is always provided as a PhysicalQuantity, where you can "choose" the unit. So when you input the mesh cut-off, you have to give both value and unit, but whether you say 75*Hartree or 150*Rydberg, it's the same. The same for output, if you ask for the total energy, it will be returned as, say, E=50.5*eV, but you can ask for the corresponding value in Hartree by doing E.inUnitsOf(Hartree).
All input quantities are converted to internal units, in which the calculations are performed. These are so-called atomic units, in which the mass of the electron and hbar etc all have the value 1 (see
http://en.wikipedia.org/wiki/Atomic_units). This means, that all energies are expressed in Hartree, automatically, and all lengths in Bohr, etc.
We don't design ATK so that users will have access to internal quantities, so you are a bit on your own there. But the Hamiltonian as extracted by the script is in Hartree, completely independently of how you specified the input.
