Right...because walking through a puddle of magical liquid that heals you when ingested due to it's magical properties should be able to work as well if you pour it out on the ground and go stand in it while wearing boots.
Boots don't keep you from being instantly affected by an acid pool or any other surface status effect.
The fact that potions work this way only seems weird because the convention in games like this is drinking them. That's still how we're all going to be using them, so I don't see this as a major problem. At least the mechanics are consistent with how other liquids work in the game world.
