The only real point I can think of is part availability. You can pretty much guarantee that 10 years down the line mankind will still have the capability to manufacture a pulse transformer, whether it be in house or externally as a custom part, but its often difficult to tell how long an IC will continue to be produced and how the prices will change in the long term.
Further to that, a pulse transformer is easy to manufacture with very high voltage withstand but is also quite predictable under faults. If a crack forms in an IC coupler then there's potential for some unexpected breakdown in isolation, if by some bizarre coincidence all the insulation disappeared from the wire of a transformer then there is still a physical separation between the windings,