This appears to be intended behaviour.  The intel-microcode package is
prepending an uncompressed CPIO archive, containing just the microcode
for the local processor, in front of the existing compressed initramfs
archive.

This is (apparently? in some versions?) supported by the kernel as an
input format to allow the microcode update to be applied early in the
boot process.

Attempting to unpack the resulting combined image with `cpio` will only
show the contents of this first archive, and not the second one appended
after it.  However, if you run `lsinitramfs` on the archive, it will
list the contents of both.

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https://bugs.launchpad.net/bugs/1597762

Title:
  intel-microcode initramfs-tools hooks mangle initramfs

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