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And fun fact: when the Pi boots up (all generations so far), the primary bootloader is the VPU (VideoCore), which then initializes the CPU and RAM.

These things are slightly weird in that way.

What does the VPU do after boot if the unit is headless?

Well you could use it for GPGPU[1], for example[2].

E.g. accelerating video decoding/encoding, OpenGL applications, etc..