Games/software have been optimized for Intel chips. Soon they will also have optimizations for the AMD chip which will level out the performance bias. makes sense to me.
In particular because of patents and copyright, despite being the same architecture (x86) a lot of stuff has to be implemented differently. In addition to siimpler stuff like perhaps different wait states for instructions, there are also wildly different implementations of the same idea, such as Intel's Hyperthreading versus AMD's SMT.
A good comparison would be how when Intel first introduced Hyperthreading, hyperthreaded CPU's would perform slower, because software wasn't properly optimized for the particulars of how hyperthreading worked. This applies here; optimizations specific to Intel's implementation of x86/x64 often won't yield the same results with an AMD processor running those same instructions.
How do you "patch" a silicon chip?
You update the Microcode, but that doesn't seem to be what they are referring to.