It took me far too long and so many re-watches over the years to apprehend that the ending of PFOR was actually Renton's dream. During the experiments performed on the pair in childhood, Eureka would appear as a long-haired girl in his dreams, able to walk in the sun alongside him.
The power that Holland & co. were trying to get her to use for them, she instead used for Renton; making his dream reality using their power (she was the lock, and he was the key) and the energy from the superweapon.
Instead of dying, she instead became 'real', because she was an 'Image' - a dream - before they returned to Warsaw. The part where the flower blooms is just the icing on the cake.
That's my take from watching it more-or-less twice a year for the past ten, anyway.
tl;dr: I'm either really slow, or a complete dumbass.