Just saw this and probably too late, did you get it working the way you want? All 3 loaders (Cfg USB Loader, USBLoaderGX & WiiFlow Lite) will work as a front end for Nintendont. I'm with you though, Cfg USB Loader has always been and is still my favorite.
The very newest version of Configurable (I uploaded it to the downloads zone a couple of months ago) does support modern Nintendont as /games/whatever [AAAA01]/game.iso (but not CISOs)
I prefer to run Nintendont directly, though - all the applicable options are there and none of the non-applicable ones are (Wii usb loaders show options exclusive to the various gamecube loaders all together)