I think you are on the wrong track
Instead of installing everything you need to cover "non Zentyal needs" then Zentyal on top of it with potential collisions, why not trying the opposite ?
Zentyal does require some web server to be installed, at least to support GUI.
For the time being, everything is merged under one single web server "brand" (Apache), even if using different configurations. (BTW, this is why I would suggest Zentyal to use another one like Nginx to support GUI..anyway)
So, it will be easier to go along with Zentyal install, including web server module and then install your CMS or whatever new application.
Is there any reason why you try to achieve the opposite ?