Path
/global_packs/required_data/Dragon Mounts Legacy/data/Dragon-Mounts-Legacy-master/src/generated/resources/data/dragonmounts/loot_modifiers/dragonmounts/water/chests

custom_w.json

/global_packs/required_data/Dragon Mounts Legacy/data/Dragon-Mounts-Legacy-master/src/generated/resources/data/forge/loot_modifiers
global_loot_modifiers.json

Issue
Format is similar between dragons. I set aether and end dragons to spawn with chance 1.0 and I've not seen them appear in end chests or any other chests. What am I doing wrong?

I've also tried replacing "minecraft:chests/simple_dungeon" to "minecraft:chests/end_city_treasure" and even that as simple as it was did not work.

Full datapack attached
Dragon Mounts.zip

Your datapack paths are incorrect, it needs to be:
Dragon Mounts Legacy/data/dragonmounts/loot_modifiers/dragonmounts/water/chests/...

Dragon Mounts Legacy/data/forge/loot_modifiers/global_loot_modifiers.json

The upcoming 1.2 version will include ways to change the chance values more conveniently through the config, if you don't mind waiting for that.