Two reasons.
First is to bring the water temp to ambient temperature so you don't shock the plant roots with super cold water if that's what comes out of your tap.
Second is that's usually done in organic gardening if you're using city tap water. Many municipalities put either chlorine and/or chloramine in the water to kill off microorganisms to make the water safe to drink. But, in the process, they also can negatively affect the microbes you are actively cultivating in your soil to help break down your organic amendments to feed the plant.
Chlorine will evaporate if left open to the air or agitated, like with an air stone, so that's what you're doing when you leave it sit out untopped.
Chloramine will not evaporate but you can cause it to instantly fall out of solution by adding a small amount of vitamin C powder.
If you aren't using organic soil for the microbes, then you are only concerned with the first issue, and frankly can use it straight out if the tap if it's close to room temperature.
Definitely want to try to halt the damage ASAP, especially if it is creeping. You could use a bit of aloe gel to seal the cut as well. The aloe has some good antimicrobial properties that could help if it is some sort of disease. Just cut off a small chunk of a plant if you have one growing in a pot or planted in your yard and rub the gel on the open stem. If you don't have a plant, you need to get one. It's really good stuff for your plants. You can blend a chunk up with water and use it in place of soap when you do your foliar sprays. It will foam up like soap bubbles but will also foliar feed your plants!
If it's some sort of tunneling bug, cutting it off a bit into the good wood and bagging and disposing of the necrotic plant tissue off site would be a good thing to do.
And be sure to wipe the blades on your cutter with isopropyl alcohol before each cut and after the last one. If it is a virus you don't want to be spreading it around to clean tissue on this plant or any plant you use them on subsequently.
And, if the problem persists even after you cut off the damaged tissue, you might want to give the JMS a go. Super easy to make and you can spray it on your flowering girls right up to harvest. But make sure you wash the buds after harvest to clean them up if you don't practice that already.
