Creating .patch-file not working with NPM overrides having (shared) nested dependency

Not sure if bug or (not yet implemented) feature.

NPM supports changing and even replacing (transitive) dependencies via the `"overrides"` node in the `package.json`, this is a NPM feature since v8 (not sure since when exactly):
* v8 documentation https://docs.npmjs.com/cli/v8/configuring-npm/package-json?v=true#overrides
* v9 documentation https://docs.npmjs.com/cli/v9/configuring-npm/package-json?v=true#overrides

I now have this interesting example where I want to replace a (transitive) dependency with a different dependency (not only a different version) in order to get rid of bugs/in order to increase build-speed/because the lib got reworked under different package coordinates:
```json
{
"name": "some-patch-package-thing",
"version": "0.0.0",
"private": true,
"scripts": {
"postinstall": "patch-package"
},
"dependencies": {
"react-use": "^17.4.0"
},
"devDependencies": {
"patch-package": "^6.5.1",
"postinstall-postinstall": "^2.1.0",
"react-scripts": "5.0.1"
},
"engines": {
"node": ">= 18.14.0"
},
"overrides": {
"magic-string": {
"sourcemap-codec": "@jridgewell/sourcemap-codec@^1.4.14"
},
"nano-css": {
"sourcemap-codec": "@jridgewell/sourcemap-codec@^1.4.14"
},
"svgo": {
"nth-check": "2.1.1"
}
}
}
```

After `npm install` all dependencies are getting downloaded, but as `magic-string` and `nano-css` are now sharing the same version, the `node_modules`-folder contain a symlink to the real package. Having two dependencies sharing the same version of a transitive dependency is KEY to this bug. Having only `magic-string` does not recreate the problem.

Here a `tree`-output of the `magic-string` in `node_modules`:
```
| index.d.ts
| LICENSE
| package.json
| README.md
|
+---dist
| magic-string.cjs.js
| magic-string.cjs.js.map
| magic-string.es.js
| magic-string.es.js.map
| magic-string.umd.js
| magic-string.umd.js.map
|
\---node_modules
\---sourcemap-codec
```

After download is finished I need to adjust the `magic-string`-package to reflect the new `@jridgewell/sourcemap-codec` coordinates, so I edit the files `node_modules/magic-string/dist/magic-string.cjs.js` and `node_modules/magic-string/dist/magic-string.es.js`.

Now here comes the problem: when I run `npx patch-package magic-string` after my edits, to create a patch-file (as normal), I will get greeted with a weird warning:

(Text version of the screenshot, to improve searchability)
```
patch-package 6.5.1
• Creating temporary folder
• Installing magic-string@0.25.9 with npm
• Diffing your files with clean files
Error: ENOENT: no such file or directory, stat 'C:\develop\tmp\some-patch-package-thing\node_modules\magic-string\node_modules\sourcemap-codec'
at Object.statSync (node:fs:1596:3)
at Object.statSync (C:\develop\tmp\some-patch-package-thing\node_modules\graceful-fs\polyfills.js:318:34)
at statSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:10:52)
at getStatsSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:24:19)
at Object.checkPathsSync (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\util\stat.js:49:33)
at copyDirItem (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:121:29)
at C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:115:39
at Array.forEach ()
at copyDir (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:115:23)
at mkDirAndCopy (C:\develop\tmp\some-patch-package-thing\node_modules\fs-extra\lib\copy-sync\copy-sync.js:110:3) {
errno: -4058,
syscall: 'stat',
code: 'ENOENT',
path: 'C:\\develop\\tmp\\some-patch-package-thing\\node_modules\\magic-string\\node_modules\\sourcemap-codec'
}
C:\develop\tmp\some-patch-package-thing\node_modules\patch-package\dist\makePatch.js:218
throw e;
^
```

This probably is due to the `node_modules` folder not existing in the one which gets downloaded on the `• Installing magic-string@0.25.9 with npm` step. I have not tested this on MacOS or Linux systems.

OS: Windows 10 Pro
Node: v18.14.0
NPM: 9.4.2