For those truly too lazy to click through to the article, x86-S stands for "simplified," with the idea being to boot directly into 64-bit mode instead of booting into 16-bit and bootstrapping to 64-bit mode. 16-bit mode would be removed entirely. It's not clear to me if 32-bit mode would be axed as well, or if it would be retained (maybe partially).
If I had to list one hundred ways x86 could be improved, not booting in 16-bit mode wouldn't be on it. It's just an incantation. There's no fallout from it. If we're talking firmware, the gigantic mess that used to be called ACPI, still leave users suffering every day for example.
If it's 2% of instruction cost, then kill it with fire. If it's raising the development cost by 1%, kill it with fire. If it's a fixed cost and isn't hurting anything, then meh.