Does it cst less to modify items at the modification stations or what is the point of them?
The cost is the same. The only thing you currently need the mod table for is to add an augment slot to an item.
Originally in beta, the tables were the only way you could add mods to gear. This changed late in the beta but the tables were not removed from the game. When augment kits were added to the game they made it required to use the tables to add the slot so they had a unique use once again.