Forerunner mutations have to be performed under the direct light of stars, and the individual who undergoes a mutation had to be completely naked. That said, the Ur-Didact's mutation in the Terminals shows him armoured - he may either have had it clothe him immediately after the mutation, or he simply had it on during which contributed to the mutation's failure. Also, I believe that the cutscene with the Librarian takes place in a place where the artificial star can be directly seen (which is why John is 'blinded' initially when the cutscene starts). You're partially right though, chemicals are used on a subject during mutations - so I wouldn't call it a 'virus', but the Didact's use of the word "inoculation" is accurate if it was indeed a mutation that John received. Physical effects of the mutation don't appear for months or years, so we could be seeing a very different Chief in Halo 5 or 6.