For my part it strikes me that there is something rather different between the thing that Eliezer ridicules and the thing that species selection can be considered an instance of.

Correct. Species don't breed - they are not part of a sexually reproducing population - so the theory and simulations ruling out group selection against a countervailing individual selection pressure (invaders take over the gene pool under all realistic conditions) doesn't rule out species-level selection. Modus ponens to modus tollens, observed examples of species selection don't argue for group selection being realistic and Phil Goetz's entire argument is a nonsequitur. This was obvious to me at a glance but experience has taught me I do not enjoy arguing with Phil Goetz.