Unfortunately, as the message in that Window hinted, this tool is only going to work for Unity’s provided shaders.
Pretty much any materials using custom shaders that aren’t specifically designed for URP aren’t going to work at all and there’s no automated way to fix that. They’d need to be re-written by hand. You can check with the provider to see if they supply URP supported shaders and materials. That’s really the only way. Many assets that are actively maintained do provide them and should state on the page which pipelines are supported.
And no, there is no way to run different objects through different pipelines at the same time. Whether you go with URP, Built-In, or HDRP you are fully commiting to it for the entire project.
