Hello! I too needed to edit some of these separately. You can use the UndertaleModTool to achieve this. Download the GUI release on the GitHub releases page. Run the executable. Then go to File -> Open -> Select Pixelart Portrait Maker's "Data.win" file. Then to export the textures, go to Script -> Resource Unpackers -> ExportAllEmbeddedTextures.csx. This will export the texture page into a folder named "EmbeddedTextures" in the Pixelart Portrait Maker's folder.
I think you can even edit the texture page and repackage it for the program to use. Though I have not tried this yet.