Almost every layer you add to Pixelmator Pro is, by default, fully opaque, meaning the layer itself is fully visible and it obscures everything beneath it. If you reduce the opacity of a layer, it becomes partially transparent, so the selected layer becomes less visible and whatever is underneath starts to become more visible. A layer with 1% opacity is nearly transparent, while a layer with 100% opacity is entirely opaque.
Note: If you’d like to save an image with transparency, make sure to export it to a compatible file format. PXD, PNG, PSD, TIFF, and GIF file formats currently support transparency.