Looking through the game with NVIDIA Nsight there are clear performance degradation during the drawing of elevated rails due to the textures having large gaps where nothing is being drawn. More info for the details can be found here: https://forums.factorio.com/viewtopic.php?p=676116

Thank you for your detailed description of the error. Currently, I am unsure of the cause of the issue, as the alpha value in the PNG files is 0 in the areas that should be ignored.
I will take a closer look at this over the weekend.

The presence of artifacts in the alpha values at the edges and corners is a result of upscaling. These artifacts are small in value and, as a result, are not visible. However, they prevent cropping.
I would be very happy if you could also take a look at my optimized version with NVIDIA Nsight. I will send you a Dropbox link via Discord so you can download the new version.