re: You make the call: safe at first or out?

Yeah I get what you're saying, and any of that could be possible. But understand that the call he made, in the way he made it, doesn't suggest any of that, and by doing it in the way he did, made the call just as bad. Out of the box is an immediate dead ball. HPU would come out from behind the plate with hands in the air calling dead ball, batter out. FU would be required to also signify dead ball. It would be nice to see the whole field in the video, or at least see a longer version of it.

If it was missing 1st base, it is an appeal play. The base runner would still be safe at 1st on the initial call. The 1st baseman would have to tag the runner returning, or call out to the umpire that the runner missed the bag (indicating it was an appeal). Umpires are not allowed to call a runner out for missing a bag or a failure to tag without the defense indicating it is an appeal to the bag for missing the bag or failing to return.