brew doctor warning about Python config scripts
The main thing it to be sure your chosen version of python is first in the path as we transition away from python 2 on macOS. 

Until you have a broken package, this is a warning and not an error, so just post your next build error with some details and we might be able to help if you have an actual problem. Also, if you have disabled SIP and changed your base OS, maybe test a clean install onto USB external drive, validate this warning doesn’t exist when you boot to the new OS and then try migrating your data over, this could just be your system isn’t “stock” enough.