The reason for not cooking all the ingredients at the same time is because different foods / ingredients have different textures, some are tougher than others, some are more porous etc. So the cooking time varies.
But, me, for most dishes I cook everything at the same time and they always turn out great - stews, curries, soups, stir-fries, beans etc.
Now using herbs for garnishing is different, this usually would be the last ingredient to add as you want it to remain fresh and 'alive' and attractive.