@ foote
I just ordered a cork board so that I can keep track of my various theories and ideas about how everything works. I'm going to go full crazy person and fill it with interlocking lines of string and hand-scrawled notations (with lots of exclamation points and cryptic phrases)
My point being, I think about this stuff too. To a truly ludicrous extent. Heartbreaker alone has had me tracing out possible variants on his chest insignia...
As for FILTER, I think that the Block might be their attempt to create an artificial Fixed Point. A stable place that they can use as a fallback when reality starts collapsing, a launching platform for their own missions, or to house people who can otherwise escape into the timestream.
As for when the riot happens, my guess is that it is substantially before the events of Vengeance, possibly orchestrated by the Baron.
Heres why...
Ra was defeated by the ennead, and goes on sabbatical. possibly this is where he ends up chained to the Wheel of Torment (seen on his incap card). The ennead were then halted by the F5, and it seems likely that some of them (including Set) could have been defeated temporarily and sent to the Block. this could give Ra the chance he needed to escape- once Set wasn't actively keeping watch, he could gather the vestiges of his power and break free.
Either way, Set is sent to the Block.
Apostate shows up. Screws around with everyone. We see Setback inadvertently punching him on Karmic Retribution (in his original costume), so its possible that this was around the time that Setback was still working with the F5. He shakes Helena's faith, but is put away before he can really do damage.
Enter the Baron. He knows that in order to exact vengeance, he needs the heroes distracted and tired. so he engineers a prison riot to help Fright Train escape. From the V5 update on the kickstarter:
After several years of incarceration, the dastardly Baron Blade managed to get word to several of The Block's inmates, Graves chief among them. "Come work for me," the Baron offered, "and I'll give you the chance for vengeance you so deserve."
So the Baron creates a situation where Fright Train and several of the worst inmates can riot and some of them can escape.
The events of Vengeance begin.
The Ennead keep Ra busy, and even though they are defeated in the process, they wear him down enough that the Baron can break his staff. My guess is that he just shaved his beard and returned to the same regalia. He kept the wisdom and perspective from is imprisonment, but decided that rags and hobo-beard did not suit him.
Apostate goes back to tormenting Fanatic. He shakes her faith, and after the baron is taken down she retreats to the monastery. this may well be where she runs into the sage, who gives her some (unwelcome, I'm sure) perspective. Once she deals with him and regroups, she and apostate have their knock-down, drag-out fight.