The desktop theme will impact scores on certain benchmarks not to mention stripping the OS and tweaks I'm not going to share. This is purely for competitive benchmarking and probably has no effect on video games though I don't know. Hardcore benchmarking is a totally different thing than optimizing a gaming PC or workstation.
You also tailor what the benchmark likes. GPU-PI for CPU is a good example. It needs XP to score high. It needs Intel OpenCL for 100M and AMD for 1B to score high. 3DMark01 is the same, XP for an extra 2000+ points but with this one the actual order you run the scenes in has a big impact on the overall score.
Some OS tweaks are not allowed, and as recently happened, they break a benchmark and it removes point scoring from it until everything is audited.