The instructions for installing simplesamlphp on Apache only require an alias for the simplesamlphp directory :
https://simplesamlphp.org/docs/stable/simplesamlphp-install#section_6
But for Apache 2.4.6+ the security has changed - it worked for me when I added a Directory directive. eg:
<VirtualHost *:80>
ServerName mywebsite.dev
DocumentRoot /home/myuser/www/mywebsite/
<Directory /home/myuser/www/mywebsite/>
Require all granted
</Directory>
Alias /simplesaml /var/simplesamlphp/www
<Directory /var/simplesamlphp/www/>
Require all granted
</Directory>
</VirtualHost>