Q: Won’t publishers make lots of variations of the d20 System concept, confusing players?
A: Sure, they'll probably try.
However, using the OGL, anyone who wants to can "fix" that content and publish the fixes, returning the variation to the core d20 system known by hundreds of thousands of gamers. And if those "fixes" are more popular than the variations, pretty soon, the "fix" will become the standard, and the variation will become a curiosity known only to a few people.
Over time, if the effort to vary the basic d20 System rules keeps failing, the number of people who attempt it will decline. At some point far in the future, commercial publishers may stop bothering to try at all.
The interesting thing about "open" projects (software, tabletop RPGs, etc.) is that they tend to suppress, rather than encourage "forks". Since everyone has the right to take an "open" project and make whatever changes are necessary to conform to the public standard, those who try to deviate from that standard are often perceived as wasting everyone's time, and being disruptive to the value of the shared community experience. Innovation happens at the edges of the envelope, rather than at the core. Changes to the core require a general consensus from large numbers of people to be successful, otherwise they'll just be ignored or "fixed" to maximize compatibility.
In fact, one of the biggest groups affected by this force will be the Wizards of the Coast tabletop RPG Research & Development team. When the time comes to make a new edition of Dungeons & Dragons, they'll have to make a very persuasive case to the market to adopt any changes to the core rules they want to make! The R&D team has already made some variations close to the core. The Star Wars rules include a different system for tracking character health, the Vitality Point/Wound Point system. Only time will tell if two variations that close to the core will both be supported by the market.