Okay so, I had 3 Giant Lotus spawn after a specific pattern happened:
I was missing only one pad to grow the correct color, I removed all the flowers/buds/seeds and the pad that has the wrong color, then I've thrown the lotus seed while using the amulet, the other day it was a giant lotus pad.
I cannot confirm that this is how it always works because, there is one that hasn't done that yet, but it may not grow a giant one because it's on the Sacred Tree area. More people would need to test this.

I have no idea, honestly. I think it's just random, but it wouldn't hurt to reset them so that they are flowerless at the same time.

Question: On the last stage, does the pads require something specific? For example, do they need to have nothing growing on them, or maybe they need to be all flowers?

I agree that there isn't much in-game information to go on, that's fair.

The rest is just intuition, I guess? Experience from playing too many similar games. :3

I do think it's pretty hard to figure out without knowing anything about it, besides that it exists. I didn't know it was a 3 x 3 grid. Could have been 2 x 2 which would have made things a lot easier. I just wished there was more info about it in the game. Maybe I've missed something. Highly unlikely but maybe.

I personally don't think it's so hard to figure out in the sense that... it's a 3x3 grid, you want one big lotus of a certain colour, it absolutely makes sense that you'd need 3x3 small lotuses of the same colour to make it happen.

Yeah, makes sense. Just unfortunate it seems so hard to figure out on your own. And here I've been like "Maybe I need to just throw one with enough space around it and it will randomly grow large".

I saw someone post a screenshot with one in the background and I thought that would be the mechanic, which was then confirmed by the dev and other people who had done it before. :-)

How did you even figure out to do this? Bruh.

AMAZING and so clear Thank you