My point is this:
Bases loaded. No outs.
Improper batter hits a grounder and R3 and R2 are out on a 5-2-5 DP.
Defense appeals and the proper batter is called out but the other two outs stand.
Three outs.
However in baseball the entire action of the improper batter is negated meaning the proper batter is called out and the other outs are nullified.
So all runners are returned to the bases loaded situation.
When you say this is the rule "in baseball", that's like saying that a rule "in softball" is always the same for USA, NFHS, NCAA, etc. Sometimes it is, sometimes it isn't.
In NFHS baseball all of the outs would stand, same as in softball.