I only skimmed the paper, which seemed to be a cool application of well established DNA profiling techniques to marine biology. Your idea is a cool one and really creative, I'd say give it a go. The theory assumes that the nem has the capability to recognize potentially symbiotic bacteria held within its stomach, prevent them from digestion and then relocalize them to the correct locations.
All of these processes are deeply involved at the molecular level. As an example, Human cells have symbiotic 'bacteria' also; mitochondria*. If you attempted to eat these in the hope of boosting your metabolic capabilities, well...its not likely they would do anything but taste bad. What I'm basically saying it might not even matter if you matched the clade correctly. All of the bacteria may be capable of inducing the response, or perhaps none of them. Its also possible the nem may rely upon dormant bacterial populations to repopulate the symbiotes after bleaching, this might mean that there isn't even a molecular process for the integration of ingested bacteria...
With that said, I am amazed by the capability of some of these marine animals to selectively transport ingested cells, the movement of nematocysts on nudibranchs is a really cool and amazing example, I would love to understand how, or read any papers that someone has...
Just my 2 cents, I work on nano-engineering applications of molecular biology, not really a marine biology guy. There is a ton of interesting papers out there published on symbiotic interactions at the molecular level. Check out NF-kB to get you started.
*Obviously no longer an independent cell, but hypothesized to be the result of a eucaryotic cell phagocytosing a procaryotic cell capable of oxidative phosphorylation. All this assumes that evolution occured of course...Hah!