hi @javipas - thank you for the feedback. Much appreciated. 
Regarding generating the zip - I was able to zip just under 3GB in around 20 to 30 min on a shared hosting so 2000 seconds should be a good base amount but if you can, try to increase it some more, maybe try 60min / 3600 seconds.
The PHP max_execution_time does however seem to be reporting correctly so maybe there’s something else on the system causing a timeout. I recommend checking the NGINX proxy_read_timeout value.
Please let us know if that makes a difference.