Right, Yanfly selection control only works within the limits of the options for targeting, which is only alive enemies. You'd need a drop-down for select 1 dead enemy in the engine before that could ever work as it is set up, as KO is considered dead by the engine, and there is no option to target KO'd enemies at all, as once the enemy is KO'd it is deleted from the targeting array so that is why Yanfly's selection control can't find them to target them. (And if they were not deleted BTW, then any attack could target them, so that is why it is done this way. Otherwise you'd have enemies wailing on KO'd party members and ignoring the rest of the party).
What might work is to use another state instead of 1 for KO, and another plug-in to count that new state as dead for purposes of Game Over. Then it might be possible to target them, but you'd have to test it first to see.