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How to create system configuration file field with allowed formats(csv/xls) validation.

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You can see an example in the native magento module - module-offline-shipping. CSV Import Field was declared in the system.xml file:

<field id="import" translate="label" type="Magento\OfflineShipping\Block\Adminhtml\Form\Field\Import" sortOrder="6" showInDefault="0" showInWebsite="1" showInStore="0">
    <label>Import</label>
    <backend_model>Magento\OfflineShipping\Model\Config\Backend\Tablerate</backend_model>
</field>

You should use a backend model to store your file in the database (or somewhere else). Example of the backend model is available here vendor/magento/module-offline-shipping/Model/Config/Backend/Tablerate.php. All magic are in this method:

/**
 * @return $this
 */
public function afterSave()
{
    /** @var \Magento\OfflineShipping\Model\ResourceModel\Carrier\Tablerate $tableRate */
    $tableRate = $this->_tablerateFactory->create();
    $tableRate->uploadAndImport($this);
    return parent::afterSave();
}

File processing is in the uploadAndImport method of the \Magento\OfflineShipping\Model\ResourceModel\Carrier\Tablerate class:

/**
 * Upload table rate file and import data from it
 *
 * @param \Magento\Framework\DataObject $object
 * @throws \Magento\Framework\Exception\LocalizedException
 * @return \Magento\OfflineShipping\Model\ResourceModel\Carrier\Tablerate
 * @todo: this method should be refactored as soon as updated design will be provided
 * @see https://wiki.corp.x.com/display/MCOMS/Magento+Filesystem+Decisions
 * @SuppressWarnings(PHPMD.CyclomaticComplexity)
 * @SuppressWarnings(PHPMD.NPathComplexity)
 */
public function uploadAndImport(\Magento\Framework\DataObject $object)
{
    /**
     * @var \Magento\Framework\App\Config\Value $object
     */
    if (empty($_FILES['groups']['tmp_name']['tablerate']['fields']['import']['value'])) {
        return $this;
    }
    $filePath = $_FILES['groups']['tmp_name']['tablerate']['fields']['import']['value'];

    $websiteId = $this->storeManager->getWebsite($object->getScopeId())->getId();
    $conditionName = $this->getConditionName($object);

    $file = $this->getCsvFile($filePath);
    try {
        // delete old data by website and condition name
        $condition = [
            'website_id = ?' => $websiteId,
            'condition_name = ?' => $conditionName,
        ];
        $this->deleteByCondition($condition);

        $columns = $this->import->getColumns();
        $conditionFullName = $this->_getConditionFullName($conditionName);
        foreach ($this->import->getData($file, $websiteId, $conditionName, $conditionFullName) as $bunch) {
            $this->importData($columns, $bunch);
        }
    } catch (\Exception $e) {
        $this->logger->critical($e);
        throw new \Magento\Framework\Exception\LocalizedException(
            __('Something went wrong while importing table rates.')
        );
    } finally {
        $file->close();
    }

    if ($this->import->hasErrors()) {
        $error = __(
            'We couldn\'t import this file because of these errors: %1',
            implode(" \n", $this->import->getErrors())
        );
        throw new \Magento\Framework\Exception\LocalizedException($error);
    }
}

PS: field's attribute type can be changed from the Magento\OfflineShipping\Block\Adminhtml\Form\Field\Import to the file if you do not want to add additional html to it.

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