You’ll still need actual supplements to upgrade each of these things as this bonus does not unlock all of them. This is understandable as these definitely would make Ellie quite overpowered early in the game.
THE HANDGUN AMMO CAPACITY UPGRADE
You’ll be able to see the Handgun Ammo Capacity Upgrade as soon as you get to the first workbench which takes place in Jackson when you’re on Patrol. It’s in Eugene’s hideout after you leave the supermarket.
You should be able to see the Handgun Ammo Capacity Upgrade unlocked straight away. This will let you hold more bullets in your handgun which is super useful as it’s probably the gun you will use most during your play through.