EA can do whatever they want to with their games. SCEA has the same right with what they produce, and from their standpoint, uniforms cannot be patched. They aren't lying to you, they're stating what they have as company policy. If you have a link to what you're referring to, I'd like to see it.
Guys, they do have to use the style guides for these things. Even though
you might think that it is a total oversight on SCEA's part, they do have to follow these things. The onus is on the individual teams of Major League Baseball, and its been that way for years. Remember when the Rangers had that God awful two toned helmet? They never wore them in game, but were in the Style Guide for years before the team finally corrected it. That was reflected in game by SCEA, and they had to because of their licensing agreement with Baseball.
That last sentence is key. If SCEA were to just go through and make whatever changes they wanted without consulting MLB Properties, Baseball would not only have the right to enforce contractual punishment on SCEA, it would possibly include the termination of the contract and could end the Show franchise for the foreseeable future. There is a point to the Style Guide: it protects the image of the thirty individual clubs of Major League Baseball. It is a point to where teams can enforce their copyrights and can market merchandise. Major League Baseball has a lot to lose if they can't even market their product. If you really want change; if you really want to vent frustration, write to the individual teams about mistakes in the style guide. Otherwise, you're going to have to live with what the team wants to style itself as.