When the texture data is stored on disk, compression (jpeg, png, etc) matters. When the texture is uploaded to video memory, the texture's compression its different -- truecolor (raw data), DXT, PVRTC. So it doesn't matter whether your source texture is PNG, JPeg, or PSD, in the end it simply doesn't matter.
GPU compression is not recommended for UI atlases. Compression is acceptable for tiled textures on 3D models, but is unsuitable for crisp, pixel-perfect UIs.