The reference you're looking for is Rule 4.09. The third out was made by the BR before reaching first base. The fact that the out was made by appeal after the runs crossed the plate makes no difference on this play since it's not a time play.
4.09 HOW A TEAM SCORES.
(a) ...
EXCEPTION: A run is not scored if the runner advances to home base during a play in which the third out is made
(1) by the batter runner before he touches first base;
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