I agree with your view that Monsanto is unlikely affected, but the article is quite misleadingly named. With "gene patent" I immediately think of Monsanto. But this ruling seems to only affect those who claim exclusive right to discovering properties of existing genes - not those who create organisms with unique genetic properties, like Monsanto.

Monsanto patents are more complicated than that though, as you can see by searching the USPTO. The enzyme is patented, the genes that produce it are patented, the introduction of those genes into a specific cultivar are patented, and crossings between their varieties and any other variety are patented. So, even if one of the patents was invalidated, the rest would still make it pretty difficult to commercialize anything.

Say you get the DNA sequence that will provide enzymes to protect from glyphosphate, and the patent is invalidated. You still have to introduce that sequence to a bacteria, introduce it into a plant in a way that expresses the gene, and then do enough crossings to make sure it doesn't interfere with the rest of the plant's functions.

So, even from the Monsanto patent, it's probably 8 years of work before you can sell anything. And by then, the market has moved forward.