You will have to test FOP2 in Elastix MT. It is supposed to work, but not really tested. The key part is the FOP2 Manager you already set your hands on, there is a functions-elastix.php file that will pull information out from ElastixMT tables and fill the appropiate data in the FOP2 Manager tables.. that is the best way to handle it. The latest FOP2 Manager has many improvements and some subtle changes for multi tenant systems, it is not yet released (version 1.0.7), but you can get it if you download version 2.29.02 beta for FOP2 that already includes the manager. AS for the way to log in, on multi tenant systems that do not use freepbx the usual way is to defined a user/pass in config.php and of course disabling use_freepbx_auth. Your modification is fine also if you want to reuse credentials for elastix in itself.. but take into account that the fop2 manager does not have user levels, the user has full privileges on all domains.
Best regards,