We do not know the engine to be used yet. Maybe they use a 3d modelling dithered down to 2d backrounds (don't know, if this the right wording). Even if you're using a 2D background you may get tiles and placeables put onto it.
But, even if creating backgrounds is expensive and hard to reach, there will be still modding possibilities like new companions, new spells, new weapons and new quest within the given areas. Well, no new campaigns as with Neverwinter Nights 1 & 2... but look at Baldur's Gate II or Icewind Dale, both are still supported by mods.
And f you look at Skyrim workshop, while Skyrim was awarded as greatest rpg in 2011 (and no, I do not agree), most mods are about god like weapons, god like armours, new companions and (nearly) naked women, even if it's a 3D modelled world. But, hopefully, we'll get better mods for Project Eternity.