I have a fresh installation of Magento2 (2.1.6) for three stores on different domains, followed the installation guide from start to finish. Apart from the Web Setup Wizard not showing up in the admin menu (seems to be a known bug noone cares about), it seems I have a much worse problem:
In theme configuration, only global settings take effect. All settings concerning the individual stores or store views can be modified but are disregarded when rendering the frontend. I tested this out by globally setting the Blank theme and Luma for a store view. All caches are disabled, I'm in developer mode, but the site still shows Blank. The same happens with meta tags or page content.
I'm new to Magento, but right at home with PHP and large scale applications, so honestly I don't know what to do anymore.
Since the issues on Github seem to be mostly ignored, I desperately hope someone can help me with this on SE.


I just solved the issue - it was unclear to me that Magento does not infer the requested shop from the URL but needs to have MAGE_RUN_CODE passed as a FastCGI param. So if anyone comes here from Google, I added the following lines to my nginx configuration:

# map the HTTP hostname to run codes
map $http_host $MAGE_RUN_CODE {
  domain1.tld runcode-1;
  domain2.tld runcode-2;
  domain3.tld runcode-3;

# pass the variable as a fastCGI param

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