Auto-gem/Enchant is for current gear, as the character is imported from the armory & doesn't take any notice of any gear in your BiB Import string... as you haven't imported it, at that point.
Once you Import the data & run BiB it takes full account of everything in your bags & what gear scope you have under BiB - this will be all available Gems & Enchants, even if you have no access to them or have a bottomless gold bin to buy them with.
BiB is like any other coding - you need to tell it your limits before it can give you meaningful results... it will also only suggest Agi. gems if Epic is set as the limit for Gems... the only Primary stat. gems are Saber's Eyes & you can only equip one, anyway.