Note that the primary publisher is not filtering at all, so as long as the primary publisher is not busy (all rendering threads in use) there is nothing preventing the primary publisher from picking up publishing tasks for the subset of Publications configured on the secondary publisher.
Maybe this is fine; in this way the secondary publisher just provides additional capacity for a subset of Publications. Furthermore, there should be a bit of load balancing going on; the chance that a publishing task gets picked up by the secondary publisher should increase when the primary publisher gets busier.
If you want a strict segregation of Publications handled by the primary and secondary publisher, you would have to explicitly configure a subset of Publications for the primary publisher too.
To ease the pain of this explicit configuration a bit: note that the "Publisher (deploying)" queue is only used for scheduled deployment and there is hardly any work to be done by the publisher for those. So, you most probably don't have to segregate On Publication for those tasks (if any).