Appeal play?

[Rufus]

This happened during our last baseball game of the season last night and we play under Fed rules.

R3 comes home on a single only fails to touch the plate (don't get me started, he should have touched the plate). There was no play at the plate or anything that would have prevented him from touching the plate (i.e., catcher wasn't in the way, etc.). The umpire called him out without the defensive team appealing.

The rule I found regarding this is 8.2.5:

If a runner who misses any base (including home plate) or leaves a base too early, disires to return to touch the base, he must do so immediately. If the ball becomes dead and the runner is on or beyond the succeeding base, he cannot return to the missed based and, therefore, is subject to being declared out upon proper and successful appeal.

I know there's been some discussion on when/if an umpire can just call the runner out so I'm not sure how that jibes with the above rule (or if there is another Fed rule that supercedes/is more appropriate). Any clarification or input would be appreciated.

For the record I'm glad he was called out as maybe now he'll be more attentive in his base running. I just want to be sure I understand the rule in this case. Thanks.