A Fatal break the build when I config my theme

**Env**

OS: macOS 10.15.6

php:
```
PHP 7.3.11 (cli) (built: Jul 5 2020 03:23:39) ( NTS )
Copyright (c) 1997-2018 The PHP Group
Zend Engine v3.3.11, Copyright (c) 1998-2018 Zend Technologies
```

**Some Code**

```php
#!/usr/bin/env php

setFileExtension(Format::HTML);
$configuration->setIndentHTML(true);
$configuration->setCustomTemplateDirs(
[
ROOT . '/docs/themes',
]
);
$configuration->setTheme('nim');

$kernel = new Kernel($configuration);

$builder = new Builder($kernel);
$builder->setIndexName('quick_start');

$builder->build($source, $target);
```

**File Struction**

* docs/
* rst/
* *Some RST file*
* ……
* themes/
* nim/
* xxx.css
* html/
* layout.html.twig

**Error Info**
```
Fatal error: Uncaught Twig\Error\LoaderError: The "/path/to/vendor/doctrine/rst-parser/lib/Templates/nim/html" directory does not exist ("/path/to/vendor/doctrine/rst-parser/lib/Templates/nim/html"). in /path/to/vendor/twig/twig/src/Loader/FilesystemLoader.php:106
```

**Expect**

I don't think it should be break when I have been specify the themes' dir.
Maybe there should be some thing make it pass as long as one of custumized dir and other per-build path.

------
Thanks for any helps!

Start with Configuration::setCustomTemplateDirs(), Configuration::setTheme(), and the Twig template-loading path implicated by the LoaderError. Reproduce the build using the PHP example and the docs/themes/nim/html/layout.html.twig structure; done means a configured custom theme directory is accepted without requiring the missing default path.

Written by the indexing model from the issue text.