emacs: fix default values of withFoo flags after overrideAttrs

Previously, the normal way to override src and version led to wrong
default values of withFoo flags.

Here is an minimal reproducible example for withXwidgets which should
default to false when version >= 30.

```console
$ nix eval --include nixpkgs=$PWD --impure --expr '
let pkgs = import <nixpkgs> { config = { }; overlays = [ ]; };
in (pkgs.emacs29-pgtk.overrideAttrs { version = "30"; }).withXwidgets
'
true
```

This fix keeps backward compatibility for the .override interface.

Fixes: nix-community/emacs-overlay#455