I have noticed that when making a custom potion, the custom effects don't override the potion's default effect. E.g., when I use the command below, I get a potion that has invisibility as well as blindness, but as I customized it, it should only have blindness.
Here's the command:

/give @p minecraft:splash_potion 1 0 {CustomPotionEffects:[{Id:15,Amplifier:0,Duration:200}],Potion:"minecraft:invisibility"}

If you think I'm doing it wrong, you're wrong. If you didn't know, they changed the potion item's format. I double checked, and looked at an item entity's NBT, and I'm right.
To test it, put the above command into a command block, and power it.
If you want to give yourself a custom water bottle, fine! However, you're also supposed to have the possibility of picking the color. A water bottle is just blue. For example, I thought gray would look good for a blindness potion. Thusly, I used an invisibility potion as base, and the custom effects should have overridden the base effect.