Yes! Programming and debugging the KIT-050 is quite the same as working with a MiniProg3. The kit has got two USB-connectors from which one is used to program and debug your project, while the other may used as an USB-connection for your your project, ie. an USBUART component.
From ( you can program via board USB or Miniprog3 interface )-
"The Kit-050 has an onboard programmer/debugger (Cypress USB chip based), which lets you program the PSoC 5 without connecting Miniprog3. This programmer debugs at a speed of 1.5mHz. The kit also allows the user to program and debug using the Miniprog3."
I would go as far as saying that programing it through the USB interface is actually easier than using a miniprog as all you do is connect the usb cable and run the programer/debuger no need to plug an aditional tool or making suer your connectors and voltage levels are right etc and even better it suppports most of the programing/debuging features of the miniprog 3.