Years go I did that always on any engine I had. Along comes the built in oiling system, separate tank and I got to thinking about what I'd hurt. So I quit. That was about the time I was on another boating forum and learned of Sea Foam. I haven't run dry nor drained the fuel system since.
My engine is 11 years old. Last fall I decided to put in a new impeller and have a look at the carbs as I was having some performance issues. I have 3 carbs and all were absolutely spotless in the bowl. The Sea Foam apparently kept all signs of varnish and all out of the fuel supply. I did find my carb problem and it was a tiny piece of fuel line lodged in the high speed jet that apparently deteriorated after 11 years of usage.
So, man does what man wants with one's money and equipment. I'm just throwing this in as a look at what might not happen if you didn't drain the fuel.
However, if I had an engine that I transported on it's side, that would be a different story and may be where I started running dry when finished.
HTH,
Mark