Well, you can't even install Blesta without phpseclib working correctly, so I don't think that an additional check in the installer is necessary. The error displayed in that case is actually quite specific. Moreover, the issue is not with CentOS per se, as we have dozens of installs of CentOS and this is not an isuse for any one of those.
Just because php can't find a particular resource being requested on the include path doesn't mean the php.ini file is configured incorrectly. While it may be the issue if you are running exactly CentOS 6.5 with php 5.4 and nginx, it is not definitively the reason.
Also, CentOS 7 has been out for quite a while, has anyone been able to duplicate there? We haven't, just FYI.