I imagine this varies by person, but thinking about a source file is already reminiscent of 2D space navigation, where the X axis is typically gated by conditions. In a similar vein, when I think about functions from different source files, I do hold some type of "depth", or "stacked panels" in my brain.

I think this is because I reason about programs being in some state ~= being positioned at a certain function with some context I carry around. I'm sure it's not the only way to think about it, but it's a reasonable abstraction over what computers do. It's how we oriented our debuggers and early IDEs on as well, and carried this over to modern tools.

Definitely something I'll be thinking about during the next few days.