As a scientist, a couple of things jump out at me about this situation.
Look at the original permit application. The original intent was to identify a coral "model species" for research.
A model species in research is a representative species chosen for ease of care, short reproductive cycles, easily identified phenotype-linked genotypes, etc. So for mammalian research, the mouse is the model species because it's easily cared for, has a 3week gestation period (pregnancy time) and short lifespan, so multigenerational genetic studies can be done in a reasonable amount of time. For simple eukaryotes the model is
C. elegans a simple worm. Or the fruitfly, the zebrafish for fish, etc.
So identifying and beginning a new model system for corals is a big deal, scientifically. Coming up with a system
and exploiting it successfully and having it adopted by other scientists is a huge undertaking, almost a career in itself.
Ok, so great.
What the hell does this have to do with the project in Florida?
If I had to guess, I would think that it wasn't to identify a single "model species" as stated in the first couple paragraphs of the permit, because if you read further you see mentioned representative species from various geographic locales. I think the vested intent of the permit application was to start up a repository-type operation like this, with the gold-standards for coral species instead of mice:
http://jaxmice.jax.org/list/rax6.html
My link is an example - a quasi-scientific but for-profit operation with mice for sale. A researcher opens the catalog, "oh i need a mouse with defect x, or with x coat color, there it is #4521! I'll take a dozen yes overnight please". So the intent in the permit seems to be along those lines, but for corals. Having restricted species/strains would be huge in terms of scientific legitimacy.
All I'm saying is that the way things went seemed to not match the permit application, the original intentions stated. As someone who has both written and reviewed grant applications and renewals and I can tell you that the permit application looks like an attempt to coat-tail a for-profit venture on an academic premise.