>There's no "picture" of all the ways that various things in a codebase will interact, design decisions, etc.
There 100% is a picture of it. Code itself is a 2D picture of logic. The picture for code is arranged in a specific way with huge limitations that don't take full advantage of 2D space.
3D space is infinite and if logical decisions can map onto 2D space (which is essentially what code is) it can also map onto 3D space.
The "language" of this mapping from logical decisions to some sort of spatial diagram can become more and more complex. Instead of linear lines of symbols (which again is what code is) it can be become a graph, or a literal pipeline of logic in 3D space. Analog computers are essentially 3D "pictures" of "code."
Additionally how the logic is represented in your brain must take up space. Logic itself is not so abstract that it takes up zero space. How ever it is stored in your brain there IS a 3D structure or "picture" of that logic that exists. If you are aware of some logical step of operations then it FOR SURE exists as a picture in your brain. I'm not saying it's a picture you can visualize... But the locations of where and how that information is connected in your brain forms a 3D structure. The essence of all logic starts as geometry in 3D space; taking away that space is the abstraction.
Code doesn't have to be visualized. Many times I don't visualize it at all. I remember it, like you... via relationships. But I have the Option of visualizing it as a picture.
If you have aphantasia it just means your brain lacks the ability to assign spatial coordinates to concepts. So you are aware of "relationships" but you can't arrange those concepts into a 3D grid and see how they are all interconnected. It's more of a disability the a brain type IMO, because people who don't have aphantasia can certainly see relationships without having the need to "picture" it.
If it does lend you advantages, I would say it's similar to how certain blind people can use echo location to navigate the world. It may lend you advantages that arise out of necessity to utilizes other tools to make up for a disability, but oftentimes it may not.