I keep my neovim config maintained by a LLM which is a fork of Kickstart.
My example might be an outlier on the easy side because they have a custom/plugins directory that will not have merge conflicts ever so I try to never modify the main init.lua and keep all of my changes separate in my own files. This prevents merge conflicts.
I can then ask my LLM to add a plugin or customize existing plugins by writing files in this separate directory to add/overwrite plugins and configurations. This works great for me.
If I were working in the main file creating merge conflicts, I could imagine it could get messy fast.