It was a Virtualmin control panel issue.
It displayed a wrong php version used by this Virtual Host.
Virtual hosts template is set to use 5.3.3 by default (user can change it later) and it is as it was displayed but phpinfo() displayed 5.6 w/o GD module.
As stated in the question, only 5.3.3 and 7.0 were installed with DG from Virtualmin repositories.
So I solved that installing GD for php5.6 from Centos repositories.
I also have to point out that from Virtualmin CP I “changed” php version to php7.0 but it seems that was not successful because WP still complained about lacking GD.
