Thought experiment for evaluating total energy
If we disintegrate a molecule one step further to isolated electrons and nuclei, will the overall energy spent be equal to negative of total energy of schrodinger equation?


By convention, yes.

Energy as a absolute quantity is not well-defined, energy must be defined with respect to an energy zero.  By convention, when we perform quantum chemical calculations our energy zero is free electrons and nuclei infinitely far apart, which we define to have zero potential energy as they cannot interact.

Also, quantum mechanically, we consider only the case at $0$ K.  We can however add on corrections to the free energy due to entropy and internal motion at finite temperatures, as well as vibration zero point energies.

How is this different from the atomisation energy?

We can see that to get from the products of atomisation to the products of "disintegration" (as you refered to it), is to remove all the electrons from the neutral atoms.  That energy is given by the sums of all the ionisation energies for each atom in the system, removing each electron one by one.  This allows us to construct a Hess cycle.

Finite temperature corrections are added to the quantum mechanical energies as the potential energy and free energy are different at finite temperature.