Not a problem. An annoyance. I ploughed on with the first draft, a mess on the pcb layout, but learnt a lot. The warning is not a problem and doesn't affect routing.
Honestly not a problem either, because now I have picked KiCad up again a little, the time it would take to add the jumpers when I add them and rename the nets is probably less time than the warnings will annoy me. (Annoyance is always a function of time - debate me).
As you say, simple circuit. I did add a few things, like the ILI9341 header etc. It's just the last time I spent with KiCad was a lot more complicated and I was just trying to avoid harassment later, by being a good boy from the start.