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)?
the best thing for n64 improvements is patience. some good improvements should be in the coming weeks/months.