While the development boards are equipped with OnBoard USB I/F, most of the real life production electronics are not (at least "mine" at work aren't). There still exists designs just using an FPGA + EEPROM w/o requiring any USB interface in target application. (In fact I'm not sure, if this USB to EEPROM I/F for programming might be w/o additional circuits useable for system communication I/F...)
In terms of area on PCB as well as production costs it's (in my point of view) a no-go to implement any (proprietary or open source) USB I/F for an one time use during production. Thus there will always be the need for a separate USB <=> EEPROM interface box for production issues.
(Yeah, this "one time required I/F" might (an will most likely) be implemented in an automated teststation for production - but what about prototyping at lab desk or system integration issues at customer site?)
Well, just as a reminder that any discussion of the need to have separate USB I/F programmers like the USB-Blaster should not focus on the need for development boards...
(IMHO the implementation on the Dev.Boards is most likely driven by the need to save the costs for any additional device in the dev.Kit. Selling the kit w/o any interface is no option
Likewise in early days of electronics.... "Connect the device xyz to the unit to establish communication with the PC (device xyz not included) :-)