That's true. I suppose I could do some edits to the OP explaining the situation between Forge and Non-Forge mods. I'll have to do that tomorrow since I'm too tired right now. When making the guide I wanted to show people how to install many of the popular mods that they've probably seen on youtube or wherever. There are hundreds of others sure, but tracking all that is a little more work than I'm willing to do. I'm hoping that if I give people access to the powerful tech mods that they can then go in and find their own mods to add to the collection. I use a few other mods that I don't list here but they're not as popular so they haven't been included.
Also, looking at the 1.4.2 compatible mod list on minecraftforums.net, the vast majority of the mods are Forge mods anyways. The mod community is going to end up gravitating towards one API eventually because mods that aren't using what the majority of other mods are using are going to find themselves not being used. You see this already happening with Forge and there are people fighting back.