I beleive you guys have really good theories on why, but could it be due to what day it was? I beleive Don got sprouted on the Dia de los Muertos; the day of the Dead. Yellow Marigolds are very symbolic during this period and are offered to dead loved ones. The scent is believed to attract the souls of the dead and bring them back.
But if that is true, the flowers only pushed Don further away from existence. (I have no clue what happens to the person after they get sprouted). And also, why would Tim Schaffer use flowers as a sign of death within death when in the Mexican tradition it is believed to bring them closer to the land of the living?
And doesn't anyone find it funny that on Dia de Los Muertos they honor the dead with candy calaveras (I've had one...not too good), pan de muertos (also a bit tasteless), cempazuchitl (yellow marigolds), and poems about the afterlife. All of these were present in the game.
And I don't want to sound like a snob pushing all this information on the board. I wouldn't even know half of this stuff if it wasn't for my Spanish teacher incessantly hammering this into my memory. Oh, and a little trip over to Wikipedia