While I'm unsure of later continuity glitches in it, it really seems like the logical time period for "Freedom Angst" is 2366, as a knowing nod to Wolf 359. It also give more breathing room for Sisko to work for Kira, as opposed to the just over one year it would be to preserve a 2369 placement. Still plugging along, watching Through the Looking Glass at the moment!
^"Freedom Angst" would have to be in 2366 to reconcile with Sisko and Jennifer being five years divorced in "Through the Looking Glass." I wonder if the 2369 reference in the historian's note was simply a typo.
As I said in the "What are you reading?" thread, I'm up through the NF stories in my MU Read through. Encountered my only continuity hiccup so far, Selar appears in Worst of Both Worlds and then again in Homecoming, as the first is set earlier they are irreconcilable. Certainly it can be read that they are two different Vulcans with the same name, but that's silly! Not a huge problem just something that cropped up. About to start Saturn's Children tonight. The Historian's note suggests it takes place between "New Cloak" and "WYLB," would I be safe in inserting it into my DS9 read order as an early part of "Season 8?" I only ask because I have a friend who hasn't done the DS9-R yet, and but he owns the MU books and was asking me how to tackle the two DS9 tales in them. (As well, I'm anal and have a spread sheet of all the novels and where I place them!)
The events in the MU don't really come into play until after Unity, so I would say wait until then to read it.