Does that apply to to self-harvested apples and berries, too? Is washing them with water a process which changes their structure and composition of nutrients? Less proteins because of less bugs and worms?

They’re selectively bred for one thing, and they start changing the moment you pick them. Just sitting on your counter changes a piece of fruit. Touching a berry with your finger introduces millions of tiny bioreactors onto its surface, some will go to work breaking cell walls, fermenting, fighting with the local and antecedent microscopic flora, and so on.

"Processing" can be a gray area

Sure, if you want to be asinine about it. The term 'processed' is probably too broad, same as calling food 'healthy' or 'unhealthy'.