A skybox is always infinitely large. You can imagine it as a sphere encompassing your whole scene. Scaling this sphere wouldn't make any difference - until it becomes so small that your model overlaps it. The size of your project appears to be compared to your skybox and is defined completely by your distance to your project.
If, for example, the buildings visible on your skybox look too large, the only solution we can recommend is to capture the image from a further distance to these buildings.
Keep in mind that there needs to be enough space from the place you capture the image to any nearby buildings for the project you're planning to create. Otherwise, the perspective will always seem off.