Aha, I forgot - that option is in 1.1.1. Also, that update changes things a bit so that the intro is smoother & less memory intensive on older devices. Hopefully it should get through review soon.
Just tried this. Played on Insula Primalis. Team was Legacy, Visionary, Haka, Fanatic, and Ra.
Vos was flipped. Fanatic took out Stalwart with Wrathful Retribution and finished off Conqueror with Absolution. No Unlock.
I have also tried the same setup as above, but on his unflipped side. Still nothing. No minions out, but the Portal was out (forgot its name).
My unlock of Cosmitron to help. Megalopolis, Legacy, Tempest, SS Tachyon, Visionary, Haka
Killed the ships separately and then savage mana'd for the unlock. Voss was on his backside, no minions, quarkdrive was out.
Did the savage mana, haka of battle combo for 78 damage (had some help from Legacy and visionary). It took forever to get the second ship out, if i did it again I might switch Tempest for wraith, however hiis early crowd control was super useful, as well as his mid/late game cleansing downpour
One possible gripe was when I dealt Tempest rampage damage (was putting a late game forced deployment's worth of minions undersavage mana), it took forever to start calculating the damage
OK, so let's work on this analytically. What do we know and what do we need to figure out:
Unlocking Cosmic Omnitron
Need:
While fighting Voss, destroy both ships (Stalwart & Conqueror) in the same round
+ Mystery Condition
The Mystery Condition does not seem to be any of the following:
Team composition - Cosmi's been unlocked using non-overlapping sets of heroes - so it can't be something unique to a specific hero. [Has anyone unlocked Cosmi without having at least one variant hero on the team?]
Fight Location - Cosmi's been unlocked in both Megalopolis and Insula Primaris - so it can't be something unique to a specific env
What else have we mentioned in this thread…
Order of ships destroyed: I unlocked after taking out Stalwart first, then Conqueror worked and Chromium got it after the other order, so that doesn't seem to be relevant (which is good as it would mess up people using Savage Mana as you can't control the order it sends things to the trash).
Who does the damage / damage type: Probably not relevant, Cosmi's been unlocked after one hero destroyed both ships and after different heroes destroyed them on subsequent turns in the same round. I've seen a couple of reports of Savage Mana unlocks, has anyone confirmed an unlock with End of Days?
Single-Shot vs. whittling: I unlocked Cosmi after single-shotting one ship with radiant damage and plinking another that was at 1hp with a projectile. Other folks used Savage Mana to discard both at once. Powerhoud took out both ships after they'd been previously whittled down. Seems like this isn't relevant, unless I'm missing something
Voss's board: Has anyone unlocked Cosmi without having Voss's field cleared? I don't think this is relevant as Carlos said he'd gotten both ships and "Sometimes it was just Voss and the ships, other times there were minons." but do we have a data point of someone actually unlocking while Voss had other cards in play?
Voss's state: I unlocked him with Super-T Warrior side up (as did others who had been taking out all the minions). Has anyone unlocks Cosmi with Voss in Warlord state? Voss had 81HP and 7 cards in his trash at my unlock.
Active Hero state: My unlock was triggered by RC Wraith doing 1 point of damage to the Conqueror. Wriath had 7HP at the time.
Story possibilities: Cosmi's bio says that a "mysterious cosmic entity" rocked Tachy's lab with "cosmic rays" which "gathered the many technological advancements of the lab together" and "bound them all together with wires and connections of pure energy." We know Tachyon's not required, but could there be another clue here? Might destroying the Quark-Drive Translocator also be relevant? Seems unlikely, but I'm trying to search for what we might have missed
Anything else?
Maybe Super Scientific Tachyon's "Research Grant" needs to be in play as well?
Unlikely as some have unlocked Cosmitron without Tachyon
I had Voss flipped, no other targets and Tempest, Haka, Wraith, Visionary (Incapped) and Fanatic in Insula Primalis. Unlocked with an End of Days. Hope that helps people narrow down the options.
Has anyone who unlocked it had at least one hero incapped at the time? So far everytime I manage to get both ships out someone dies before I can kill both.
Is it possible that there is a hero that isn't allowed to be present?
Has anyone unlocked it without a promo hero on the team? Because I see a lot of fails without a promo specified, and every success has one.
So much for that idea. Got both ships out early. End of Days with no one incapped. Nothing...
Just had a (separate) thought: If someone has to uninstall and reinstall (say they upgrade their device), will they lose their variants? 
I have failed to get Omintron while having 5 heroes in my group with one incapacitated (both ships killed).
I have failed to get Omnitron with only 4 heroes in my group no incapacitated (group was Legacy, Tempast, SS Tachyon, RC Wraith) - both ships killed.
Not sure what I am missing have failed a total of 4 times with diffferent teams. Killed both ships in a single round all 4 times. Twice killed both ships in a single turn.
I would guess answer is yes. I have to unlock them seperately on each of my two ipads.
Has anyone successfully unlocked Cosmin-O with End of Days? Maybe that is part of the problem.
EoD causes destruction during the environment turn. Maybe the ship destruction needs to be during hero turns? Have not yet been able to test this though...
I believe there are confirmed instances of people unlocking it without SS Tachyon (or regular Tachyon) in their team at all.
Someone said earlier they got the unlock with end of days. I've killed both ships now with Tachyon, SS Tachyon, Wraith, and RC Wraith. With end of days, and without it.
Incaps - There's a screenshot on Twitter of someone unlocking Cosmi while on an incapped hero's turn, and muliple people have unlocked without any incaps, so that doesn't seem to be relevant.
Promos - The interesting point in NumberSix's post is failing to unlock Cosmi after killing both ships in a round with at least one Variant hero in play. That seems like it eliminates "Need to have a Variant" as the missing condition (unlesse there's more to it).
Like phantaskippy though, I would still like to hear of someone unlocking Cosmi without using a promo hero, just to be certain.
I unlocked Cosmitron without using promos. My team was Legacy, Tachyon, Wraith, Haka and Fanatic. No incaps. No minions, and I killed the Quark Drive a couple of turns before.
I believe Wraith took out the Stalwart with Throwing Knives after it had languished at 1hp for most of the game, with Haka one-shotting the Conqueror the next turn with Savage Mana. Interestingly, it didn't unlock when I put the ship under Savage Mana but I rewound and corrected that mistake and it worked.
The rest of the game was... interesting. All heroes were at 2-4hp, Voss was at 43. And I won. Yeah!
How many forced deploments have folks had in the villain trash? My success, I had all three. My failure, one or none (unsure). I had one "boom tube" in the trash.