It's not possible to put a custom design on your Island Designer app and plant a flower on top of it? You could use the dark dirt and put flowers on top if you want. I don't know what else you could do.
I mean, on the bright side, yeah, people can use them to control their flowers... but it'd be cool if custom patterns in general had settings you could toggle, like whether plants/things can grow through them or what sounds they make when you step on them