Ok finished my Empire Aflame, Filos, Iron-Maiden, no scaling, Hero (Normal) mode run with a score of 1040, and a loss on the final scenario (so 23 scenarios completed, 18 on time). Scoring may be broken in Empire Aflame (assuming Empire Aflame is the only campaign with generators) since you are awarded for units killed (around two thirds of my score came from units killed), and you can just leave a unit generator alive and milk it indefinitely. I say may, as it could be the case that generated units don't contribute to scored kills. There could also be a similar exploit with AIs that hire units, which would affect other campaigns as well, so an alternative fix which would handle both is to award no score for killing units "over time" (which again, may already be the case, I don't know).
Playing against monster generators is a lot more fun than playing with monster generators, as they are effectively a time pressure mechanism -- at the very least you have to always be killing more than N units a turn where N is the number of generators (each generator spawns 3 units every 3 turns, so effectively 1 unit a turn), or if the primary objective isn't to "kill all opposition" (as the game puts it), you still need to be making steady progress towards the goal, lest the battlefield get swamped.
Personally, in the two scenarios where the enemy had generators (not counting the final, the demon gate, and the one in which they first appear where your goal is to escape), I used my air force on march orders to go for the jugular i.e. the generators themselves, and then the Spawns which could re-establish them. Shadowspawn only have two units with anti-air capabilities, the Shadow Worms (?) (rare), and the Shadow Beasts (? I may be misremembering these names) (even more rare), which I would prioritize on my path to the generators, making the aftermath of this strategy a tedious purple lobster (the fourth kind of Shadowspawn, I believe they are called Shadow Claws) hunt across the map, with absolutely no way to lose a unit as they simply could not fight back against my Night Mare Acolytes or Reapers. The first time it was mildly amusing even though tedious, the second time, it was old, thankfully there wasn't a third time. The fix here would have been to make these missions "destroy all generators" not "kill all opposition".
On the other hand, playing with monster generators is not fun because you end up with dozens of trash units you need to laboriously concentrate in order for them to be an effective fighting force (my original plan, which I somewhat stuck with, was to use an entourage of Shadow Spawns to set up 3 generators ASAP, and then have Spawns be my infantry, while I only maintained an airforce). Alternatively you can use them as expendable scouts for recon and exploration, but it's no less tedious -- the tedium is a result of the way generators are established with no way of relocating them (or even destroying them, AFAIK. Why is there no way to fire units during a scenario?), and the timing with which they spawn units. A fix could be for them to accumulate spawnable units at the current rate (or some adjusted rate), but only actually spawn them on demand, and to be able to transfer units from one gate to the other. But, to be honest, best would be to just keep generators strictly in the hands of the enemy. Since I doubt the devs will ever revisit this and modders tend to never cut, only add (if they ever even appear for this game) your best bet as the player, right now, IMO, is to just completely ignore shadow essence.
As for my final scenario loss, ironically, being shown part of the enemy's force composition during the deployment phase contributed the most, as I thought the separate groups manning the wall could be aggroed separately, but turns out they aggro all at once. As a result, my strategy which involved (what turned out to be an overconfident) charge with my air force into the eastern most shadow spawn group was subsequently flanked on both sides, and instead of retreating, I decided to breakthrough to the primary objective (as I suspected the forces would be thin behind the front line, which they absolutely were not), took too many losses, and it was over.
I did manage to get the secondary objective with a small infiltration detachment (Longbowmen, Trackers and Armored Archers with an invisibility cloak), which gave me control over all generators on the map. Only a small respite from the shadow spawn onslaught, as the generators are promptly taken out, and (assumedly) re-established. I guess it can give you 6+ turns of no spawns in a mission with a 30 turn limit hard timer, so it's not that bad a prize.
Even with that experience, I'm not sure the strategy I've formulated for next time would work either, which is to distract the bulk of the enemy forces with spawns, while a larger infiltration group consisting of my elite air force as well, gets the Transmuter's College (aforementioned secondary objective) and then from there launches an assault on the primary (the Master). That said, I don't know when next time will come, as a replay of the Filos route is now my bottom priority for this game.
I want to try the main campaign next, then maybe Moira route.