If you go by what Rioters have said outside of the lore it starts to make a bit of sense what they tried to do and where they originally planned for the story to go.
When the Pantheon lore dropped and let's just say there was dissent on the boards over the quality and direct of that lore Rioter Jaredan basically tipped his hand and straight said "Atreus's story is not over."
However, when discussing Targon lore it has been repeatedly said that the Aspects choose how much of the host's individuality to overwrite. With Taric being stated to be the one with next to no influence of the space parasites on his personality, and Atreus being completely taken over. Leona and Diana somewhere in the middle.
So, it's probably more accurate to say that Atreus is now trapped inside his own body, rather than just being dead with his spirit in their version of heaven. This actually follows with a completely different Rioter (Waaarghobo) claims about the afterlife in Runeterra, essentially stating that there is no heaven the souls get reincarnated.
As to why Pantheon is following what Atreus wanted to do originally, well, the boy wanted to go to war and kill things. He's possessed by a spirit that is known for going to war and killing things. There's gonna be some overlap there.
As to a more meta textual reading as to why the lore focuses on Atreus. Well, probably because the writers didn't even know what the space parasites completely were when they wrote the first round of Targon stories. According to Diana they're some group consciousness collective thing. According to Pantheon and Leona's lore they're some part of the beings the human Targonians worship as gods, which is somehow connected to the stars. According to Sol they're not gods they're this magical species of enslaving upstarts that built a space empire off the back of forcing him to do their dirty work and murder his friends and siblings.
It isn't until over a year later with the Darkin rewrite that we get the idea that they're actually all tied to some fundamental function of the human experience. To me this reads like it's just been finalized what they're actually going to be doing with the story. So of course Pantheon's lore couldn't focus on the space parasite itself.