I just generated my first *.bin from the online configurator and it worked fine on Windows.
I didn't change much, just created a new layer so the left Alt key behaves more like Fn so I can press F1-F5 without requiring my right hand, and also so left Alt+L/R arrow keys map to Home and End (this has been a godsend coming from a decade of macOS!).
Could you elaborate more what issues you were seeing? It's also worth noting that the instructions on this page are a bit dated, seeing as you don't need an additional keyboard to flash the firmware anymore. It was really quite simple!