Okay so some things to note:
Every plant has 3 levels Mild, Normal, Potent.
After your plant is a potent level 3 producing 10 ea of that plant per harvest it has a chance to mutate.
The chance of mutation seems to be very tied to game progress. I had a toxic leaf that wouldn't mutate until I killed the Hollow Knight. I had close to my toxic leaf cap at the time, should have mutated long, long before.
I would suggest leaving the entire left side garden un-planted until you can fill it with level 3 plants. That way it's closest to the door i.e. crafting. After plenty of harvesting you won't ever need to touch any of the other plants again, so focus level 3's together. When you uproot you retain the seed but have to regrow from level 1 when replanting.
I have replanted a couple plants to see if it's possible for a second round of mutation, but I'm guessing it's a NO.. that's a big no.. This game wants you to have a grueling grind not a pleasant one, it's free after all. Speaking of grueling.. STEAL, am I right.. so worthless. That ability was in old school rpg so you could steal an epic secret or otherwise unable to get items, not so you could just get some ingredients that can be easily payed for, in a game that doesn't even have selling options?.. Don't waste time stealing, it does nothing for the game, just makes slow battles even slower. I mean who's running out of money? How? Where can I buy Energized or Group Haste, or let me steal it. How are they going to give us awesome items in a tournament to use nowhere else in the game...What?!? rant, rant, rabble..