I think this just furthers the idea that Ella isnt manipulating the situation as much as some people claim (Being MC dad, faking her friendships for almost a decade etc). Ella allegedy does all this stuff to MC but then when she gets to know MC (personally know MC since she had to do research/interact with MC as dad) she is willing to put her entire plan at risk? No matter if you are as kind/understanding/of the same mind as she is? While it hasn't happened yet we "know" that at some point we are going to be given a choice to side with her or not/kill her or not/fulfill her plan or ruin it so that means Ella is willing and able to have a decade long plan involving governments and extremely powerful people but then almost instantly is willing to throw it away for love (again even if you pick every "negative" option with her like you dont like your powers etc).It's possible that as time goes on Ella starts to like the MC more and decides that she'd rather not murder him to absorb his mutations, or that could just not be a possibility..
I really dont get why (not you personally) people are seemingly so gung ho on the idea that Ella has been orchestrating everything? Unless Ella can get a 6th evolution we know she wont be the "final boss". To me it seems like it would be a Madara/Kaguya scenario from Naruto. You have Madara/Ella a villian people love who basically manipulate the whole series in the background only for some borderline godlike entity like Kaguya/whatever Ella is working towards to come up beat the better written villein and then lose to a 20 something loner and his harem (Team 7 or the girls in this game).