Enchanted soil hasn't prevented decay for a very long time by now, and the Hydroangeas is explicitly not affected by the speed-up either. All other flowers with a fixed effect interval do get the boost (except Dandelifeon, which may change in the future, though).
The pressure plate setup you describe has a limit on how fast it can output items, so the number of endoflames it can supply depends on the burn duration of the fuel. You will have to experiment with your options, as far as fuel and mana collection are concerned. If you need to scale up past those limitations, you might as well look into other generating flowers.