>>105334208I can see both the "big sister" and "two kids who fell in love via traumatic experience" angles, and I think both are correct. Memo's inclusion muddies it a bit since she does give him eyes and kisses him on the cheek(probably planned so as to not weird out normies). I say through out the movie bee and charlie see each other as friends, but some time around third act(personally, I think its when she resuscitates bee with the electro guns) they begin realizing feelings for each other. Specifically, charlie realizes it immediately but doesn't think much of it until she calms bee down during the shootout with the soldiers. Bee may have realized it then too, or when the moment he puts her in the dumpster for safe keeping(I would hate for anything to happen to her). Either way, they survive the battle with the decepticons, and when she sees him sink her gut tells her to go for him(you don't hesitate when its the one you love). When they see each other under water is when they both realize their relationship together, and they swim up with each other in a shot that totally apes from The Shape of Water(bit on the nose, but I still think its a beautiful shot and it makes me tear up a bit).
Then, at the end when they say their goodbyes, they're also breaking their short lived relationship apart. Bee wants her to come along, but knows she can't, and she wants to either go with him, or for him stay with her, but she knows that's not feasible. So they admit to the responsibilities they must see to, and how they can't incorporate each other into their lives, and move on.
This is when memo comes back in you see. When he goes to hold her hand, she tells him no, "we're not there yet" ( I needn't remind you how many times she hugged bee). This is because she is still reeling from the breakup and she doesn't want to move on quite yet.