I was able to separate my Drupal 8 database from my CiviCRM database fairly easily, here are my notes I took on how to do it. Note that these steps aren't particularly specific to Drupal 8, and can be used to convert any single-database install into a two-database install.
Create a new database (e.g. "example_civi") on the same server.
Do NOT create a ...
We totally gave up on using sub-groups with the CiviCRM Multisite. This is too bad but really this seems to be far too complicated and very risky. That would also damage the work of people using different sites.
We use only the Domain Group S-group for Site S to be sure we have the right contact in the right site.
So I found the problem.
Thanks to @HomoTechsual who lead me in the right direction.
The reason had been found in the Settings - Outbound Mail.
It was set to mail() with a success message : Your SENDMAIL settings are correct. A test email has been sent to your email address.
That looked good but in fact the message was never sent by the server ! Trusting ...
What finally made it work was this:
First I needed to set the CIVICRM_SETTINGS env variable to the civicrm.settings.php file for my subsite
Only then could I execute the php file export.php, not with src but with php-script
drush php-script /var/aegir/platforms/...
To execute a PHP script in the context of a selected site, use drush php-script or drush scr.
In your question you specified the site using -s example.org, and I suspect you may be looking for -l (--uri) rather than -s (--simulate) to determine which site to load. See the first section of drush help output for these flags.
If -l doesn't do it, you can also ...
Thanks Jon G, for steering me in the right direction and hopefully this might help someone down the line.
I probably wasn't particularly clear in my description in that I run a Drupal multisite but CiviCRM is still running under it's original single site (although this is bringing me a step closer to having all the sites run CiviCRM especially for webform ...
A fix for multisites and Aegir setups will come out in CiviCRM 4.7.21.
The fix for our problem ended up being somewhat multidimensional.
The patch in https://issues.civicrm.org/jira/browse/CRM-19303 solved the issue of the autogenerated path for the [civicrm.files] variable in 'Settings - upload ...