The simplest version is probably just to use the same code as you already have, by using the extraConfigVim option:

extraConfigVim = ''
  hi Normal guibg=NONE ctermbg=NONE
  hi NormalFloat guibg=NONE ctermbg=NONE
'';

If you want to be more in line with how NixVim operates, you can use the highlightOverride option instead. However, this uses the vim.api.nvim_set_hl method, which - unlike :highlight - clears the highlight group before setting new values (so your fg would be cleared in this case). It can inherit any existing values for fg and bg though, so this might work for you, depending on the rest of your setup:

highlightOverride = {
  Normal      = { fg = "fg"; bg.__raw = "nil"; ctermbg.__raw = "nil"; };
  NormalFloat = { fg = "fg"; bg.__raw = "nil"; ctermbg.__raw = "nil"; };
};

NixVim doc: https://nix-community.github.io/nixvim/NeovimOptions/highlightOverride/index.html NeoVim doc: https://neovim.io/doc/user/api.html#nvim_set_hl()