Yes. And also the fact that most foods float (to the top) which makes the liquid seem more obvious at the bottom. The experienced canner, especially those that want to submit their creation for judging at a County Fair, perfect ways to keep those issues to a minimum.
Me....I just give the jar(s) a shake after they've cooled and the contents will spread out a little and not look as strange.
For some tested and approved recipes such as found in the Ball Blue Book offer a choice between doing a "raw" pack or a "cooked" pack. With pre-heating the shrinkage occurs before the food goes in the jar. Pre-heating is extra work and often is not worth the effort if you have a lot to process.
Support bacteria. It's the only culture some people have.