Real product versus toy: The arduino libraries are not the standard AVR libraries you would use to program a real product. In a real product you would also never use an arduino, too expensive and bulky.
Also, the arduino ties up a bunch of pins and space compared to just the chip, for not much payoff in a typically sharp focus microcontroller use case.
I think the cost for a programmer is a wash when you consider that you only need to buy bare chips after you learn how to use the programmer.