There is an additional mesomeric effect, which is closely correlated witb the inductive one.
When phosphoric acid is singly deprotonated, the negative charge is delocalized, and thus stabilized, through pi backdonation from the unprotonated oxygen atoms (shown here with negative formal charges as in a model with no $d$-orbital contribution) to the sigma antibonding orbitals. This is shown in valence-bond form in the top pair of resonance structures below; since sigma antobinding orbitals are involved the hydroxyl group on the bottom is displaced from the covalent bonding. With pyrophosphoric acid, shown in the bottom, a hydroxyl group is replaced by a dihrogenphosphate group, which better accepts the negative charge. This enhances the charge delocalization and further stabilizes the pyrophosphate monoanion.
[Note: my device does not gave good enough drawing software to render these structures, so I had to resort to a screenshot.]