A tunnel can be seen as one hole or two holes depending on how you look at it, amirite?

I disagree. You are trying to use a 2d concept to explain a 3d occurence. A tunnel AKA cylinder It is just a hole with depth/height. Your typical 2d hole is a cylinder without any depth/height.

No, it's 1 hole.

There's no wall to separate the two holes, therefore it is just one long hole.