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Starlight is still in the unclassified defense budget, so I would imagine it is still in the classified part as well. On the website, they state that Spire was developed for the Intel community, so I would imagine they are still using it also.
I think Lt. Col. Shaffer said they were using info from both classified and unclassified databases. Shaffer said they were using eight data sets to get the info, so it would have been probable the different variations of a name could be linked. It's been a long time since I've written a nested query, but they could put in all sorts of "where x = y" statements, look at the results and end up using good old gut instinct to weed out the different name spellings. In a less formal fashion, genealogists do this all the time.
But...notice the different results you get when you google "Tony Shaffer" (909 results) or google "Anthony Shaffer" (39,400 results). Now do an advance search within "Anthony Shaffer" results and add "Information Dominance Center" (404 results). Now add "MacDill" (3 results). All depends on that first search uncovered, doesn't it?