There is no in-universe "story" explanation for this, negative energy is just more important for undead
The school description for Necromancy says:
Necromancy spells manipulate the power of death, unlife, and the life force. Spells involving undead creatures make up a large part of this school.
Aestetically it is of course entirely unsatisfying to have an assymetric treatment of positive and negative energy in school choice. Negative energy cures undead as listed in the description for the Undead type, but that positive energy hurts them is not listed there:
Negative energy (such as an inflict spell) can heal undead creatures.
Positive energy still damages them, so that is symmetric, but this is listed in only in the text of individual spells that conjure up positive energy, such as cure light wounds:
Since undead are powered by negative energy, this spell deals damage to them instead of curing their wounds
There are many effects that could be put into multiple schools. If you conjure something that affects undead, it could go into conjuration or into necromancy, depending on what you see as more important.
From the treatment of the undead type that only mentions negative energy, and even from the explanation in the cure spells, and with necromancy being the school of all things involving undead, it appears 3.5 edition expresses that manipulating negative energy in any context is more strongly tied to undead than moving it around is tied to conjuration. Without negative energy, there would be no undead at all, while without positive energy to harm them, they could still exist. Positive energy, while it also can affect undead, is not as inherently tied to them, and there is no vivomancy school for healing in the system to put it in, so it was put into conjuration.
Earlier editions treated all kinds of healing, animating and raising the dead as necromancy, so the assymetry here in a way is caused not by inflict spells being necromancy, but by cure spells being moved to conjuration, a move that was never executed all the way with the other aspects of conjuration being fleshed out for positive energy.
I don't think there is another "story" or lore aspect to it. 3.5 does not have a one-world, one-universe story background, even if it had a default campaign setting in Greyhawk. The system was supposed to be a general, and each campaign world could have their own backstory and rules how things work in different ways, as examples like the Eberron campaign setting show.