A partial answer for Toru Hagakure and an unsupported thought for Koji Koda. Bottom line is we don't know, but we can make some pretty good guesses.
As with Mineta's case, it is pretty straightforward to score points. As mentioned in the author notes you've provided,
And remember that the rules of the Entrance Exam was to immobilize or render the villain-bots unable to function anymore, not necessarily destroy them.
IIRC, there was a switch off button on the Villain Bots, which Hagakure used to disable them and hence pass the entrance exam. Will try to find the source.
Also, her quirk is more than transparency/invisibility and is some sort of light manipulation as seen in the Provisional Hero Licences Arc, where she
blinded a group of participants using the light from Aoyama's Laser.
Now, Koji can talk to animals and order/request them to help. In a city setting, while it may be tough, I think he would communicate with animals such as rats/birds to help him immobilize the Villain Bots. Birds attacking sensors or rats eating through the wires.
Another thing that we may be missing is Rescue Points. Each individual's overall score is unknown, but we do know that everyone but Bakuro (Only Destroyed) and Midoriya (Only Rescue Points) scored a combination of both points. Since both these individuals are shown to be very "nice", I'd assume they got their fair number of rescue points.