I was't able to find a better solution via a quick search so I decided to write this script. It's a simple python3 script with no external dependencies that runs apple scripts to save and apply layouts. You can have multiple layouts for the same resolution saved under different names.
Currently it only tracks one window per app since that covered my needs. Feel free to make a PR if you'd like to help add support multiple windows.
I'd love to hear your thoughts. Please leave a comment below and let me know if you've found it helpful!