Replacing a DC barrel connector with a molex connector?
Dc barrel connectors are suitable for external connections. Shrouded connectors like you link to are not. They are for internal board to wire connecting. There is also amperage concerns, but the RPI and other board you link to do not use high current supplies.

You can replace the Barrel connector of you want. But if you want a quick connection, the RPI can be powered via usb or through the header connection without needing to desolder the barrel connector. Not sure if the RFID board has a direct 5V input on the lone header, but the silkscreen on the lower unpopulated headers seem to indicate that they can be used, once you solder in a header. Check it's schematic if available, or use a multimeter.