I find it’s a good idea to make a bunch of markers for mods I expect to see in play, with simple names like (say) “frozen” (for Cold effects) or “dazed” (for getting confused with Banter or zapped by a Suggestion) and fill in the actual value of the mod as its produced, but I’m playing face to face so you might need less prep than I do. Not every mod will apply to every situation (being frozen might not hinder a psionic Overcome, for ex) and technically the entity that applied the mod can choose when to use them, but if you’ve got a lot of them in play it may be a good idea to just ignore that and always apply them at the first chance. Players (and GM NPCs) can also remove a mod with an Overcome or opposed mod (Boosting to counter a penalty) but mostly you only see that when there’s a persistent mod in play.
Your villain a Domain archetype, or maybe a Titan? They can both trigger environment twists, but it does take their action to do so so that keeps it reasonable - they can’t use their other abilities (barring reactions) and still kick the environment into high gear. Depending on what other abilities they have your players may need to be careful to stay on top of keeping the environment minions under control, those abilities where you roll any number of their dice and use that to attack everything but the Domain villain or even just heal him can be game-ending if there are too many minions in play.
Remember that when a villain ability triggers an environment twist the scene tracker doesn’t advance as well, so they can’t speed up the clock - well, unless one of the major environment twists says to advance the tracker, but even then those aren’t repeatable so it’s pretty limited. IIRC the Domain ability lets you pick your e-twist from the current zone or the next one up the GYRO ladder, so you can start throwing Yellow e-twists at them right away if you want. The Titan version is limited to the same zone, I think.
If they wreck the zeppelin (as I expect they will) next session maybe you could do a follow up adventure down the line where the Nazis send this goofball villain from my blog for revenge:
The Colossal Z-Man
Heinrich there would be at the top of his game in WW2.