There is no interface to control the relationship from menu to domains.

1. +++ b/domain_menu_access.info.yml
   @@ -2,8 +2,16 @@ name: Domain Menu Access
   -version: VERSION
   -core: 8.x
   +# version: VERSION
   +# core: 8.x
   

   this change is wrong

   only version should be removed

2. +++ b/domain_menu_access.info.yml
   @@ -2,8 +2,16 @@ name: Domain Menu Access
   +# Information added by Drupal.org packaging script on 2017-02-07
   +version: '8.x-1.0-alpha1+0-dev'
   +core: '8.x'
   +project: 'domain_menu_access'
   +datestamp: 1486480985
   

   use git as source so you never get packaging data in patches

3. +++ b/domain_menu_access.module
   @@ -51,41 +51,3 @@ function domain_menu_access_form_menu_link_content_form_alter(&$form, FormStateI
   -function domain_menu_access_form_domain_access_settings_alter(&$form, FormStateInterface $form_state, $form_id) {
   
   +++ b/src/Form/DomainMenuAccessSettingsForm.php
   @@ -0,0 +1,81 @@
   +class DomainMenuAccessSettingsForm extends ConfigFormBase {
   

   imo bad idea, better to use menu edit form alter

1. +++ b/domain_menu_access.info.yml
   @@ -2,8 +2,16 @@ name: Domain Menu Access
   +  - options
   

   domain_access already depends on options module, remove

2. +++ b/domain_menu_access.module
   @@ -51,41 +51,3 @@ function domain_menu_access_form_menu_link_content_form_alter(&$form, FormStateI
   -function domain_menu_access_form_domain_access_settings_alter(&$form, FormStateInterface $form_state, $form_id) {
   ...
   -function domain_menu_access_form_submit(array &$form, FormStateInterface $form_state) {
   

   menu_ui module could be disabled so better left as is just change config name

1. +++ b/config/schema/domain_menu_access.scheme.yml
   @@ -0,0 +1,4 @@
   +
   

   nit, useless extra line(

2. +++ b/domain_menu_access.info.yml
   @@ -2,8 +2,9 @@ name: Domain Menu Access
    dependencies:
      - domain
      - domain_access
   +  - menu_link_content
   

   domain_access already depends on domain

Thanks for the patch to add the config to the menu's. But I was missing the links to get to the admin form. So here is a patch that also includes the menu link and task link.

Apologires for wrong patch. Included is the correct patch

Fixed typo in patch.

The patch #13 is not completely working.
Attached new patch based on #13

Done