If I was the base ump and some dingbat tried to overrule my call.... I'd have had a discussion right then and there. And when we were done the runner would be safe.
Runners colliding at a base is not interference. Especially when the first baseman is backing into an area where he thinks the base might be located.
Was there a double base - I see some mention of it? If the 1st baseman was properly standing on the inside (white) bag, not backing over both bags, and the batter runner decided to use the white bag instead of running unimpeded through the outside (orange) bag... now I've got some issues. Runner can be called out for using the wrong bag. Maybe I misunderstood, but it didn't sound like this was the situation.
My partner is going to get vocally lambasted in front everyone and when I'm done, we're going to have incidental contact, dropped ball, and a safe runner.
I've never overruled a base umpire since it happened to me - probably 15 years ago.
