Spine has added support for ProRes encoding since version 4.1.21-beta, which includes the ability to export with alpha transparency by checking the "Transparent" option. However, specific support for ProRes Proxy as an encoding option is not mentioned in the available contexts. While ProRes support is available, it may not specifically include the ProRes Proxy variant. If this specific codec is crucial for your workflow, it might be worth exploring the current ProRes options in Spine to see if they meet your needs or continue using external tools like Shutter Encoder for further encoding.