If I use view component like the document says

return [
    'components' => [
        'view' => [
            'theme' => [
                'basePath' => '@app/themes/basic',
                'baseUrl' => '@web/themes/basic',
                'pathMap' => [
                    '@app/views' => '@app/themes/basic',
                ],
            ],
        ],
    ],
];

does it means that the main.php in the folder @app/themes/basic/layouts/main.php will replace the main.php in the folder @app/views/layouts/main.php ?

and how yii2 achieve this? I couldn't figure out though I traced the controller to find something which could help me understand the logic.

I traced the codes as following, but I didn't find out how the layout main.php been replaced when using themes.

1.SiteController, default action index, then render the view

public function actionIndex()
{
    return $this->render('index');
}

2.call the Controller class function render

public function render($view, $params = [])
{
    $content = $this->getView()->render($view, $params, $this);
    return $this->renderContent($content);
}

3.get the yii\web\View

public function getView()
{
    if ($this->_view === null) {
        $this->_view = Yii::$app->getView();
    }
    return $this->_view;
}

4.use the View class function render

public function render($view, $params = [], $context = null)
{
    $viewFile = $this->findViewFile($view, $context);
    return $this->renderFile($viewFile, $params, $context);
}

5.find view file, get the view file path

protected function findViewFile($view, $context = null)
{
    if (strncmp($view, '@', 1) === 0) {
        // e.g. "@app/views/main"
        $file = Yii::getAlias($view);
    } elseif (strncmp($view, '//', 2) === 0) {
        // e.g. "//layouts/main"
        $file = Yii::$app->getViewPath() . DIRECTORY_SEPARATOR . ltrim($view, '/');
    } elseif (strncmp($view, '/', 1) === 0) {
        // e.g. "/site/index"
        if (Yii::$app->controller !== null) {
            $file = Yii::$app->controller->module->getViewPath() . DIRECTORY_SEPARATOR . ltrim($view, '/');
        } else {
            throw new InvalidCallException("Unable to locate view file for view '$view': no active controller.");
        }
    } elseif ($context instanceof ViewContextInterface) {
        $file = $context->getViewPath() . DIRECTORY_SEPARATOR . $view;
    } elseif (($currentViewFile = $this->getViewFile()) !== false) {
        $file = dirname($currentViewFile) . DIRECTORY_SEPARATOR . $view;
    } else {
        throw new InvalidCallException("Unable to resolve view file for view '$view': no active view context.");
    }

    if (pathinfo($file, PATHINFO_EXTENSION) !== '') {
        return $file;
    }
    $path = $file . '.' . $this->defaultExtension;
    if ($this->defaultExtension !== 'php' && !is_file($path)) {
        $path = $file . '.php';
    }
    return $path;
}

6.render this view file

public function renderFile($viewFile, $params = [], $context = null)
{
    $viewFile = Yii::getAlias($viewFile);
    if ($this->theme !== null) {
        $viewFile = $this->theme->applyTo($viewFile);
    }
    if (is_file($viewFile)) {
        $viewFile = FileHelper::localize($viewFile);
    } else {
        throw new ViewNotFoundException("The view file does not exist: $viewFile");
    }

    $oldContext = $this->context;
    if ($context !== null) {
        $this->context = $context;
    }
    $output = '';
    $this->_viewFiles[] = $viewFile;

    if ($this->beforeRender($viewFile, $params)) {
        Yii::trace("Rendering view file: $viewFile", __METHOD__);
        $ext = pathinfo($viewFile, PATHINFO_EXTENSION);
        if (isset($this->renderers[$ext])) {
            if (is_array($this->renderers[$ext]) || is_string($this->renderers[$ext])) {
                $this->renderers[$ext] = Yii::createObject($this->renderers[$ext]);
            }
            /* @var $renderer ViewRenderer */
            $renderer = $this->renderers[$ext];
            $output = $renderer->render($this, $viewFile, $params);
        } else {
            $output = $this->renderPhpFile($viewFile, $params);
        }
        $this->afterRender($viewFile, $params, $output);
    }

    array_pop($this->_viewFiles);
    $this->context = $oldContext;

    return $output;
}

7.if the theme is not null, the system will call the $this->theme->applyTo($viewFile) to get the theme view file, and renderPhpFile

$output = $this->renderPhpFile($viewFile, $params);

8.get the content of this file

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This happen because when Yii2 perform a render check in config / components the real mapping for views container direrctory.

This can be related to all the views as in your case

    'view' => [
        'theme' => [
            'basePath' => '@app/themes/basic',
            'baseUrl' => '@web/themes/basic',
            'pathMap' => [
                '@app/views' => '@app/themes/basic',
            ],
        ],
    ],

or can be related to some vendor or modulo as

'view' => [
     'theme' => [
        'pathMap' => [
           '@dektrium/user/views' => '@backend/views/my-view-user'  // mapping per overriding s dektrium  views with personal  views 
         ],
     ],
 ],

you can take a look at reference doc for views http://www.yiiframework.com/doc-2.0/yii-base-view.html

and https://github.com/yiisoft/yii2/blob/master/framework/base/View.php