I was looking at the pathfinder craft alchemy skill and I have to ask, why are arrow, raining (or raining arrows) listed there? Their loaded with holy water which to my knowledge isnt an alchemy substance. Holy water should be divine in nature.
It is alchemy, but not a very spectacular kind of alchemy.
A Raining Arrow is described as follows:
This thick-shafted arrow contains a reservoir of holy water and is designed to burst upon impact.
From my personal experiences arrows do not travel very far when fired with something hanging from them. So the only way to deliver a liquid payload is to take a hollow arrow and fill it with said payload. You'd need to pour holy water into the hollow shaft, which will involve instruments to carefully do so because it's a more delicate version of trying to fill a bottle with a bucket. So you'll be wanting delicate instruments to fill the shaft, seal it up and use the shaft to fletch yourself an arrow.
Secondly, Holy Water exists in something of an unusual spot as a pseudo-magical item. There are plenty of adventuring items that cause unusual effects such as Sunrods, Smokesticks, Tanglefood bags and such.
Another point of consideration is at a single Raining Arrow costs 30 gp. A single dose of Holy Water costs 25 gp, so 5 gp remain for the hollow shaft, arrowhead and feathers. It is not unthinkable that these items cost about 5 gp, assembly included. So Holy Water is not made while making a Raining Arrow, it's an ingredient.