Several reasons.
1) Their reputations. Not getting mods at all would hurt their reputations, while limited mods with severe limitations imposed by Sony will shift blame elsewhere. Some were blaming Bethesda for the state of PS4 mods. Few can reasonably do so now.
2) Legal reasons. Mods were mentioned in the game description in the Playstation store, so failure to deliver them at all could open them up to lawsuits.
3) It gets their foot in the door. Having established mods for the PS4, the inequities between the PC, Xbox and PS4 modding scene might very well pressure Sony into giving a little more leeway.
4) Skyrim SE will now sell more copies.