Hi everyone,
I thought I comment as it worked for me (playing on PS4).
I cleared all nettles, dandelions and thistles (weeds) but ONLY around the bottom section which is full of Eyebrights and the middle section which has mint.
I did NOT clear anything in the top section (surrounded by planks from 3 sides) which has Comfrey as Nicodemus only mentions Eyebright and Mint. I also didn’t pick up any weeds above the third section which only has nettles, dandelions and thistles. I went to Nicodemus afterwards and told him i’m done. He then went to check the garden and said that it wasn’t perfect but good enough and the quest was completed.
Make sure you check for dandelions as they are oftentimes hard to spot. Hope his helps!