I think that we have to read the missed-base cases correctly. In the first case you cite, R1 acquires 2B but misses it, and more or less immediately turns around to touch the base. J/R's point here is that the action is unrelaxed at 2B, since the runner is immediately trying to correct his error there. Tagging him out then would NOT be an appeal, consistent with J/R's philosophy about unrelaxed action around a missed base. So it also cannot be an advantageous 4th out appeal.
In the second case you cite, R1 has NOT stopped himself to correct his baserunning error, but has instead proceeded to 3B where he is put out for the 3rd out of the inning. His baserunning error is thus still appealable, in this case for an advantageous 4th out. Although the 3rd out was in a sense "unrelaxed," since it was a live-ball play on a runner, it was not unrelaxed in the strict sense of a runner scrambling back to touch a missed base.
Hope that helps.
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Cheers,
mb
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