You know, I have always wondered if that was the case, then why did the following happen:
1) She at the beginning of the game had chosen Jake, James and Kenny. If she was serving the 3rd and 4th, and they wanted an avatar, why bother with those 3 then? During the frat party she even asks herself if it really had to be the MC. Now Jake I understand was a potential chosen for Authority, I doubt Body or Memory would let her chosen (Ella according to you) serve Authority's goals.
2) Didn't she tell the Body to fuck off once she reached LVL 5? That she was going to do things her own way? I don't know, I doubt she serves those two apostles at all and she wouldn't be the first one, we have seen Aos and Sylas not being fond of their apostles, so being a chosen doesn't mean that they have to follow their wishes. The 6th wants Aos killed after all.
With that being said, it would be dissapointing to not have a final clash between Ella and the MC, regardless of their relationship (hateful or romantic). I feel Ella herself could become the avatar of evolution since she can eat monsters/humans the same way the MC does. If MC loses that fight she could eat him and become evolution.
Well, first James and Kenny were monsterfied spawn of the Myniak, and the Myniak is a descendant of either the 3rd or 4th, this makes sense since you can make that giant Myniak submit to you if your corruption is high enough, and when it submits it sees either the 3rd or 4th in your shadow and it submits.
As to why Ella bothers with Jake....it's because whilst she is the chosen of the 3rd and 4th she, atleast on the surface, serves the goals of all Apostles, which is to find a perfect avatar through a perfect spawn.
This is true for most chosen other than Aos, Valravn and Sylla, they all are exclusively loyal to their creators but they serve the common goals of all Apostles in one way or another. So yes, whilst the Apostles have some rivalry and grudges between them ( as seen if you consume Jake, you see the first quarrel with the 3rth and 4th ), I think all Apostles at the surface work towards the same goal, so yeah I think Body and Memory would not go out of their way to prohibit their chosen from serving the goals of another Apostle.
This theory that Apostles share the same goal is in my view solidified by the fact that Ella, Aglaeqwif, Eisheath and to an extent, the Rebis, all chosen of different apostles, have a shaky alliance going on and all have helped eachother throughout varios points in the story, Indra would likely also help them if he wasn't such a hardass. If Apostles were so openly hostile to eachother they would not let their chosen work together, but they do, because they have the same goals.
Meanwhile, the outliers are Valravn, the chosen of The Lord Of Dark, who is hostile to all other Apotles and Aos and Sylla who chose to abandon their duty to further the goals of Apostles in exchange for their own personal goals, and paid the price for abandoning their common cause.
And SPOILER FOR THE LATE GAME :
Why do you think Indra, a chosen of Power, would be so offended and hellbent on revenge because Sylla ditched her duty to Memory ? Because Apostles share the same goals, and so do their chosen.
And lastly, sorry but I'm lost here, when did she tell Body to fuck off ? I can't for the life of me remember.