I use this rack sitting on the bottom of my water bath/pressure canner. You do not want the jars sitting on the bottom of the canner, that direct contact can cause the jars to break. This raises them enough so its not a problem. Yes, the jars touch each other. That's never been a problem, whether water bath or pressure canning, whether quarts, pints, or jelly glasses. Sometimes pints and jelly glasses are mixed.
If you want to overthink it and get technical, it's better for the water you put the jar into to be warmer than the jar. When air warms up it expands. When air cools off it contracts. That's how you get the seal whether water bath or pressure canning. The air (or liquid that turns to steam) escapes through the lid/ring when you are processing. When the jar cools it contracts and creates a partial vacuum, which creates the seal.
With your salsa you probably have a very small head gap, but you still have one. If the water is cooler than the jar, that can cause the air inside the jar to compress, which leaves a partial vacuum. It's possible that could cause some water to find its way into the jar. If the water is warmer than the jar the opposite happens, the air expands and keeps the water out. It's a stretch, I know, but theoretically it is possible. That's why, when you wash fresh eggs, your wash water should be warmer than the egg. If the water is colder, the air cell in the egg could shrink, creating a vacuum and sucking water and maybe bacteria inside the egg. Commercial egg packaging operations make sure the wash water is a few degrees warmer than the eggs.
Egg shells are a lot more porous than the lid/ring fit on your jars. The more difference in temperature inside the jar to outside, the greater the pressure. Also, I assume you wash your equipment and use clean water. I would not worry about the water being dirty any more than I'd worry about eating off the dishes you washed as long as you rinse the soap off. This is something I don't even think about when canning. But if you are searching for something to worry about, have your water a bit warmer than the jars.
To summarize. Since texture isn't an issue I can't see any real reason the water needs to be boiling when you start. Just have the water warmer than the jar.
