Home manager neovim: Run extraConfig after plugins have loaded?

Before I moved to home-manager I had a init.vim with some things before vimplug’s imports and some things after. If I move those things above the imports stuff breaks.

Now I’m trying to move to home-manager and neovim plugins are not in the init at all, but rather in the plugins section of programs.neovim in home.nix. Now my autocmd!s are being run before before plugins load properly and they have no effect.

home.nix init.vim

Specifically coc-rust-analyzer is fighting with the indent settings.

How do I either stop RA from touching my indent settings at all or get the autocmds to run later? I have asked on r/neovim too, but to no avail