I suspect they do it this way rather than manufacture empty packages because there are a huge variety of chips out there with an equally diverse set of package designs. It's easier to pay unskilled laborers to sort chips into 200 different groups based on size, color, and pin count than to build a machine to replicate 200 different package types.
That's the crux. You don't buy mass-produced empty packages to put the parts in. Packaging happens by putting the IC die, pins and bonding wires which connect them together inside a mold and filling it with plastic.
It's probably cheaper and certainly lower-tech to replace markings on existing chip than produce a new one.
I suspect they do it this way rather than manufacture empty packages because there are a huge variety of chips out there with an equally diverse set of package designs. It's easier to pay unskilled laborers to sort chips into 200 different groups based on size, color, and pin count than to build a machine to replicate 200 different package types.