Comment # 6 on bug 1023616 from Petr Gajdos

sysconfig.d/* files are now included separately on the httpd command line in
start_apache2, sysconfig.d/include.conf is now included via -c parameter,
instead of -C parameter. That should solve your issue.

If a need to include vhosts.d/* after sysconfig.d/include.conf will arise, then
vhosts.d dir could be also included on commandline instead of httpd.conf if run
from start_apache2 and from httpd.conf otherwise (IfDefine !SYSCONFIG).