It is more the first than the second. The magazine "Kingdom" piece shares an author and themes with the Empire from 3.5, but the two are otherwise entirely separate adventures.
This version roughly doubles the page count of the 3.5 version, and uses a similar underdark map. However, it assumes that the ghouls failed in their plots of the 3.5 version, and presents an entirely new storyline, new monsters, new magic, and new twists. At the time of the 3.5 version, Kobold Press was a very new company, and so that work is also only modestly illustrated in B&W.
Basically, this uses the same locations and the same ghoul culture, but tells and entirely different story on a much larger scale and with much better design, editing, playtest, and graphics.
Familiarity of the prior version of "Empire" is not required in any way to run this campaign.