My quick question is, since the 4.6 official image is a couple of months old, if I really want to make sure to start from the best basis, does it suffice to run the «update packages»?
i would, but generally you shouldn't update unless there's something specific you want. and, as always, take a backup.
Does it covers everything there is to update? And are there things worth updating from source to get latest improvements (especially if regarding n64 performances)?
see https://retropie.org.uk/docs/Updating-RetroPie/#binary-vs-source-updates
the best thing for n64 improvements is patience. some good improvements should be in the coming weeks/months.
