You can indeed use items that you give them as offerings for the construction of their altars. Also, It is absolutely okay to use the items that you have for offerings for your companion like crystals and stones, If anything, it'll mean more because those stones will have your personal touch to them, they will have a deeper meaning. They will act as physical points for helping in all aspects of your life which at the end of the day, our companions want nothing but the best for us.