That's the peculiarity of the RPG Maker perspective.
Some things actually don't look good when a "correct" perspective is applied.
Look at the road tiles for example. They don't have a different width whether they're horizontal or vertical. That'd be the same with railroads.
Sure, it looks more like a bird's eye POV, but it still looks OK because I can't "see" the 45°. There's no vanishing point and the top of the screen doesn't show a narrower view than the bottom.
Since your railroad is done without a visible perspective angle, it doesn't look like you intend it to look like.
A lot of text, sorry. I'm not sure how to explain in english what I mean.
I understand what you tried to do, but the engine doesn't work like a real world 45° angle camera.