The reserve levels are there to prevent your freighters (and/or mass drivers) from taking away minerals you want to keep on a body.
For example if you had an extra-solar mineral hub consolidating all the mined materials in its system and also functioning as a fleet base, you could set your reserve levels to 1000 of each mineral. Then a freighter sent to the base with a 'load all minerals' order would take whatever it could without reducing the base below its reserve levels.