Spine never modifies your image files. That would be surprising, it's better you fully control your image files.
When you scale your project, it scales everything in each skeleton that has a size: bones, meshes, etc. However, region attachments are sized based on their image file size. If you resized your skeleton but didn't resize your images, your region attachments will still appear the old size.
The reason some attachment appear the right size is that mesh attachments aren't based on the image file size. Each mesh vertex has a position and the vertices determine how the mesh image is deformed. Scaling the skeleton scales the mesh vertices, so the size will match the rest of the scaled skeleton. The image the mesh uses is the same, which may be larger or smaller than the mesh vertices.
Generally you should resize ALL your images to match the scaled skeleton. There are some instances where it can make sense to use different sized images, but it's somewhat rare. For example, a large explosion might use a lower resolution image that is stretched very large.
