Yes, it has come on a couple of times. Because I was breaking it in, I did not go very far, so there were gas stations nearby, and I filled it up. I'll start keeping better track of the mileage. I have been focused more on getting it properly broken in than anything else. I have heard that the float is prone to ethanol damage, but I'm pretty sure mine is still too new for that.
Is the fuel pump made by Keihin? I saw a post from a while back where someone used a part from a Keihin pump to repair a broken RE pump. Keihin pumps are used on many Japanese bikes, and I have never heard of problems caused by running out of gas before. I have an EFI Yamaha scooter, and it does not have a warning about running it out of gas. Also, all EFI cars use similar pumps, and as a former fleet mechanic, we would get a call every once in a while from someone who had run out of gas. These pumps would fail occasionally, but it was not common, and I never noticed any connection between pump failure and running out of gas. I worked for the same place for 36 years, and never heard this even mentioned, or saw it in any manual. In fact, most car pumps will shut down if the system loses pressure.