I understand completely, but it doesnt actually change the balance of anything. If i want to power my entire Botania ecosystem off a few endoflames I can do that. In fact, on most servers I find the players build a bunch of hydrogengas, plop them next to infinite water, and that is their Botania power forever. They never progress any further in generational plants, you even see youtubers doing this. There is absolutly no requirement for progression in Botania Mana generation other than a drive for larger, more efficient Mana generation...
Vazkii somewhat fixed this in a recent update. Passive flowers now decay over two days until they disappear completely.