Custom theme block position is not importing
The solution was to disable and un-install my custom theme and then re-enable.

Here are the steps (Where vcs is our directory for default config defined in settings.php and my_custom_theme is our theme name).

After running drush si, lets import our config.

drush cim vcs --partial -y

At this point although our config has been imported our custom blocks are not appearing in the regions as set in the config .yml files.

Enable a core theme so we are free to uninstall our custom theme.

drush cset system.theme default seven

Rebuild the cache now.

drush cr

Uninstall our custom theme.

drush pm-uninstall my_custom_theme -y

Enable our custom theme.

drush en my_custom_theme -y

Set our Custom theme as default theme.

drush cset system.theme default rrre_theme -y

Import our default config.

drush cim vcs

Run Server.

drush rs

:)