Not entirely sure about reporting this one, but it only seems to happen with your brews.

It seems that when MFR overrides the Milk Bucket (which is its default behavior), the Milk Bottle from it does not clear potion effects from Botania's Brews. (at least, not normally)
I tested this by drinking a Flask of Gills, a Potion of Fire Resistance, and a Blood Magic Potion Flask with the Regeneration effect. Afterwards, I drank a Milk Bottle, and though the other potion effects disappeared, the Water Breathing was still there.
After exiting and reloading the world, the Milk Bottle was able to clear the Water Breathing effect, but not those of another flask I had just drank.

The Flask of Sane Thoughts did have its effect cleared by the Milk Bottle. After chugging all the flasks, I determined that it was the only one.
The normal milk bucket will clear the effects as expected, and when MFR is not set to override the milk bucket, the milk bottle seems to work on the effects of your brews.

I'm also wondering if I should tell Skyboy as well.

Vanilla milk clears it fine, I don't do anything weird with my potions.