• uses NVIM_APPNAME to differentiate from other neovim instances. It's set to neovim-pde or neovim-pde-hm for home-manager (configurable).
• when running/using neovim-pde from the flake directly it runs in 'isolated' mode. Without going into much detail, this means that it append its config in nix store to your $XDG_CONFIG_DIRS and use -u flag to force-load this specific init.lua. This means that any init.lua in your local $XDG_CONFIG_HOME/$NVIM_APPNAME won't be loaded, even if $NVIM_APPNAME is neovim-pde (I think that after folders and others that don't need to be required explicitly will be loaded, but I've never tested this). That also means that exrc functionality won't work (eg. .nvim.lua files won't be loaded automatically). If you rely on that feature (I do) then consider using the provided home-manager module.
• if isolation is not what you want, then use the home-manager module, which links the configuration to your XDG_CONFIG_HOME folder and loads it from there.

Inspired by:

• https://primamateria.github.io/blog/neovim-nix/