I watched the first episode of Season 4 this morning, and based off of that, at least the first of the two episodes pretty much has to take place before it and the Season 3 finale. I haven't watched the second extra Season 3 episode, but from the description on Netflix it sounds like it takes place entirely in an alternate universe.
As I recall, the episode kind of tiptoed around the cliffhanger and hinted that it might have come sometime afterward. The idea at the time was to mix these episodes into season 4 where convenient, as they'd done with the extra episodes shot for season 2 and sprinkled through season 3; so if season 4 had been on FOX, it probably would've been slotted in a few episodes after the premiere. Yes. However, it does work as a thematic coda to the season or even the whole series up to that point.