Same behavior here:

Server version: Apache/2.4.18 (Ubuntu)
libapache2-mod-fastcgi Version: 2.4.7~0910052141-1.2

Also 
Header always set My-Custom-Header "Some content"

is not working.

Fastcgi is defined like:

FastCgiExternalServer /usr/lib/cgi-bin/php7-fcgi-www -socket
/run/php/php7.0-fpm-www.sock -pass-header Authorization

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https://bugs.launchpad.net/bugs/1368308

Title:
  Apache Headers could not be set

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