I think the thing to remember is that it isn't necessary to the game to understand this. The guides that have been uploaded that some people use to help them aren't official parts of the game. They were just things that have been discovered by paying attention to cross-breeding and mutating plants.

Many of us started this game without any aids or guides and we've been able to find the Magic Plants by just making lots and lots of cross-breedings and see what results.

I created my own breeding charts (that didn't use the magic order) and I'm used those to check on what will result if I cross a Fabled Rare Oak with a Spotted Maranta. I then checked another list to see if that result will give me a plant combo that I haven't seen before. (I'm way behind Charley, but in one of my games, I'm at 225 species discovered...)

Before I found all the Magic Plants, I used this method (on several games at once) to find holes in my "all games all species" chart to see if that new combo will result in what I want! I made an exception when a new trial combo resulted in a nw (for that game) Magic Plant that I already knew about.

It turned out in the end, that the last two I needed to discover were found using different methods. One was found while recording Mutation data, the other happened to be a seed I bought from the Supply Store!

As one of the Faucet Tips says, there are many approaches to solving the game.