is there any way to keep free contributed plugin (for example MageMonkey 2) to be enabled across different instances of website(dev, stage, prod), keeping the configuration?

Suggested solution:

I've managed situation by adding required module to composer.json of my custom administrative module managing dependencies to another modules and adding UpgradeData.php with update script.

More detailed explanation:

Code structure

|--app/

   |--code/

      |--<My Vendor>/

         |-- ...

         |--<My Module>/

            |-- ...

            |--Helper

               |--Configuration.php

            |--Setup/

               |--UpgradeData.php      # save custom module settings here

            |-- ...

            |--composer.json           # module's composer file

|-- ...

|--vendor/

   |--<ContribVendor>/

      |--<ContribModule>/

|-- ...

|--composer.json                    # home directory composer file

|--auth.json                        # can be gitignored

Module composer.json sample

{

  "name": "<My Vendor>/<My Module>",

  "description": "N/A",

  "require": {

    "php": "~5.6.5|7.0.2|7.0.4|~7.0.6",

    "<Custom Vendor>/<Custom Module>": "<Module Version>"

  },

  "type": "magento2-module",

  "version": "<My Module version>",

  "license": [

    "OSL-3.0",

    "AFL-3.0"

  ],

  "autoload": {

    "files": [

      "registration.php"

    ]

  }

}

Upgrade script sample:

<?php

namespace <MyVendor>UpdatesSetup;



use MagentoFrameworkSetupUpgradeDataInterface;

use MagentoFrameworkSetupModuleContextInterface;

use MagentoFrameworkSetupModuleDataSetupInterface;

use <MyVendor><My Module>HelperConfiguration;

class UpgradeData implements UpgradeDataInterface

{

  /**

   * @var <MyVendor><My Module>HelperConfiguration

   */

  protected $config;



  public function __construct(

      Configuration $config

  ) {

      $this->config = $config;

  }



  /**

   * {@inheritdoc}

   * @SuppressWarnings(PHPMD.ExcessiveMethodLength)

   */

  public function upgrade(ModuleDataSetupInterface $setup, ModuleContextInterface $context)

  {

      $setup->startSetup();

      try {

          if (version_compare($context->getVersion(), '<ModuleVersion>', '<=')) {

              $this->config->setMyModuleSettings(); # Implemented in HELPER below.

          }

      }

      catch (Exception $e) {

          print $e->getMessage();

      }



      $setup->endSetup();

   }

 }

Helper script sample:

<?php

namespace FFWUpdatesHelper;



use MagentoConfigModelResourceModelConfig;

use MagentoFrameworkAppHelperContext;



class Configuration extends MagentoFrameworkAppHelperAbstractHelper {



  /**

   * @var MagentoConfigModelResourceModelConfig

   */

  protected $config;



  public function construct(

    Context $context,

    Config $config

  ) {

      parent::__construct($context);

      $this->config = $config;

  }



  /**

   * Helper to set <My Module> settings.

   */

  public function setMyModuleSettings() {

    $this->config->saveConfig('<Config key according to schema.xml of module implementing config - ContribModule in our case>', <Value>, '<Scope>', '<ScopeId>');

  }

}

Final step

I my CI i run 2 steps on each deployment - during development:

magento setup:upgrade

magento setup:di:compile

Disclaimer

Do not forget to add your api keys for contrib module to composer auth.json file (or any other authentication method for composer).