"Shadow variant" has no real meaning in Neverwinter Nights; the spells cast via greater shadow conjuration are identical to their "normal" versions, except they have a different spell level. This includes the spell school with regards to considerations such as spell focus and arcane defense (only relevant for the web subspell). In particular, the innate level of each variant is the innate level of the corresponding "normal" spell (4 for summon shadow and minor globe, 2 for acid arrow, ghostly visgae, and web).
One advantage of this spell is having five spells combined into one. For sorcerers, this effectively increases the number of spells known. For wizards, this provides the ability to select which spell to cast at the time of casting.