The downgrader PUP is official and made by Sony to do some special stuff because of security-related stuff post-3.55 (everyone should be familiar with Sony's panic and 3.56)
Once you downgrade to 3.55.001d, you can simply reinstall your regular patched DEX firmware.
After you run norunpack on the dump, open the eEID and metldr with a hex editor and verify it isn't full of zeroes.
That's certainly interesting. It seems to load SELF/SPRXes into memory and proceed to dump them. IIRC a member here on PS3News suggested that taking memory dumps of DEX machines running games to get to the EBOOTs, but I'm not sure how viable that is (pretty sure they're kept encrypted in memory and decrypted only before execution)