Let's all agree that the formula $ \frac{1}{2} \iiint \rho_{macro} V_{macro} d\tau $ is a decent approximation to the work done to build this system of charges (basically a considerably large charge distribution).
Let's say I have a charge distribution, I calculate the work done to build this (approximately), by considering it to be made of macroscopically small but microscopically large blobs of charges, over which we average the true charge densities to get the macroscopic charge densities. The formula $ \frac{1}{2} \iiint \rho_{{macro}_{1}} V_{{macro}_{1}} d\tau $ would give us the work it takes to bring each one of these blobs from infinity to its prescribed point.
Now let's reconfigure this system into one which has a totally different charge distribution, shape, etc. The work it takes to freshly build this new configuration by bringing each one of these blobs from infinity to their new prescribed points would be $\frac{1}{2}\iiint \rho_{{macro}_{2}} V_{{macro}_{2}} d\tau $. Can we simply say that the work it takes to reconfigure the system would be the difference between the two integrals $\frac{1}{2}\iiint\rho_{{macro}_{2}} V_{{macro}_{2}} d\tau - \frac{1}{2} \iiint \rho_{{macro}_{1}} V_{{macro}_{1}} d\tau $?
I ask the above question because when we calculate the work it takes to go from one configuration to another, we must also consider the difference between the total sum of the self energies of these blobs but the above integrals (by definition) don't take into consideration the self energies of these blobs.