Firstly, Mr Mack sums up the trilogy for us: "In terms of its story, the trilogy is about Starfleet, the Federation, and our heroes facing their greatest threat, the Borg, in an all-out clash of civilisations. As far as its theme, it’s about the need for hope."
"Within that framework, each book also has its own thematic idea. The first book, Gods of Night, is about the way that violence often seems to be self-perpetuating — or, as expressed in the words of Bertolt Brecht, ‘Der Krieg findet immer einen Ausweg.’ (‘War always finds a way.’) The second book, Mere Mortals, is about the way that we are each our own prison, and the way that we reflect and eventually personify the qualities of our confinement. The final book in the trilogy, Lost Souls, is about finding nobility in the very struggle of life itself."
And also explaining the some of the setting: "It is a major crossover event, but it principally involves series set during the 24th century: Next Generation, Deep Space Nine, Voyager, Titan, New Frontier, Corps of Engineers, Klingon Empire, and more. The parts of the story that take place in other timeframes don’t have a direct link to the 24th-century plotline…At least, not at first."
"Different parts of the trilogy take place during different timeframes. The primary story, which features our major characters, transpires over the course of approximately seven days. In the first book, "Gods of Night," the flashback story covers several months during a different century. Book two, "Mere Mortals," has a flashback storyline that covers more than 850 years. The last book of the trilogy, "Lost Souls," features a flashback tale that covers a period of a few months in the distant past."
He also talked about the development process, just getting the outline for the whole trilogy done took six months. When Mack and his editors finally approached Paula Block for approval she asked for no changes, but ominously asked "Are you sure you really want to do this?"
Once that was done tying in the trilogy with the rest of the Trek-litverse took some effort, two editors were involved; Marco Palmieri (who oversees DS9, Voyager, Titan and Klingon Empire) and Margaret Clark (TNG and Enterprise). Mack also made the effort to coordinate with the writers of works set before and after the trilogy to keep everything consistent: "In many ways, we have begun treating the writing of Star Trek novels like running a writers’ room on a television series, with the editors serving as showrunners and each of us doing our part to tell the individual stories while safeguarding the continuity and narrative cohesion of the franchise as a whole."
The Unreality SF interview also went into some depth on Mack's other work, including quite a lot on the development of the Vanguard series, particularly how the series managed to develop it's back and forth rhythm of authorship (between Mack and Dayton Ward & Kevin Dilmore): "Marco, Dayton, Kevin, and I met over lunch one day during Shore Leave a few years back and discussed the notion of turning it into a back-and-forth game of one-upmanship. The idea appealed to all of us. It was an approach that hadn’t been done much before that, and we all felt that we worked well together. And so, this crazy little conspiracy was hatched."
He also mentioned that James Swallow's Mirror Universe: Shards and Shadows short story "The Black Flag" will be a Vanguard story. And on that note Marco Palmieri recently made a post on the TrekBBS detailing which series will be in the anthology, in addition to that Vanguard tale and a mirror-captain April story there will be: "Enterprise, the original series, The Next Generation, Deep Space Nine, Voyager, New Frontier, Stargazer, Gorkon, Titan, and one more that's outside those classifications, but which may be considered TNG" One of which will be by David Mack.
For lots more detail on Destiny and David Mack see the articles at TrekMovie and Unreality SF.