When I set custom apache directive: It does not work. In "public" folder I put index.php with simple phpinfo() and I receive error: Apache log: File is created, I have checked this. Apache vhost:
The file you posted looks as if you edited it manually, it has not been generated by using Custom Apache directives function in ISPConfig. The Docroot is overridden by ISPConfig by adding a second DocumentRoot line at the end, in your case, the first line has been changed and the second one is missing, so clearly not a vhost with oevrriddem docroot from ISPConfig. Btw. I just tested it and Docroot overriding works fine.
I should mention that only .php files are "File not found". HTML are loaded just fine. Is this may be related to PHP config in vhost?
Solved: When setting "Chroot PHP-FPM" is set for website Custom docroot does not work correctly (may be related to PHP-FPM settings in vhost).
This is a known issue. I have been fiddling with it a lot, but have not been able to find a 100% working solution (yet).