The chorus fruit cooldown indicator bar appears to have its maximum height set based on the default cooldown time rather than the time for the current cooldown. This can be seen by creating a custom item with the "chorusfruit" cooldown_type but a different cooldown time than the default (20).

Prerequisites:

A custom item with the following behavior entity json definition file:

{
    "format_version": "1.12",
    "minecraft:item": {
        "description": {
            "identifier": "flippy:test"
        },
        "components": {
            "minecraft:stacked_by_data": true,
            "minecraft:use_duration": 1,
            "minecraft:food": {
                "cooldown_type": "chorusfruit",
                "cooldown_time": 100,
                "nutrition": 0,
                "can_always_eat": true
            }
        }
    }
}

Reproduction steps:

1. Give yourself multiple custom items and put them on the hotbar

/give @s flippy:test 10

1. Give yourself multiple chorus fruit and put them on the hotbar

/give @s chorus_fruit 10

1. Eat the custom item
   1. Custom item cooldown bar fills the hotbar slot as expected
   2. Chorus fruit cooldown bar extends up past the hotbar
      
2. Eat the chorus fruit
   1. Custom item cooldown bar is small – does not fill the hotbar slot
   2. Chorus fruit cooldown bar fills the hotbar slot as expected