Yes there is a harmless explanation. The VIA C3 is a fairly simple CPU design that cracks x86 instructions into an internal simpler instruction format. Some complex x86 behaviour is normally implemented by lengthy microcode or complex state machines. VIA wanted to make their CPU simpler than Intel and AMD. To do that they exposed this internal instruction set to the BIOS to let it handle hardware initialisation and documented how to lock this feature safely away afterward. Some BIOS authors didn't read/understand the full specification. shrug.

IIRC there are also a few hints they at least considered exposing this alternative instruction set at runtime to get more performance out of the CPU core e.g. more useable registers, more three operand instructions, saturating and packed math for DSP workloads, etc.

I was wondering the same, this is an ancient CPU by now, having been introduced in 2001. During development and at the introduction, most people were still running Windows 95/98/ME, which had more serious security issues (like every user essentially being admin). It may just have been a handy (debugging?) feature?