The writer of the episode, Adam Mallinger, said on Twitter that Lara's line, "The Kryptonian consciousness will remain in the Eradicator, and their powers will dissipate over time," was meant to explain how the Smallville residents survived the fall. To me, it's not communicated well (the line seems almost like a non sequitur where it's placed in Lara's dialogue), but apparently they retained their invulnerability long enough to be unharmed. It also takes care of the question of whether they'll keep their X-K induced Kryptonian physical abilities (they won't).
It's weird that the X-Kryptonite did two very different things.
1. Gave Kryptonian powers.
2. Allowed for the transfer of consciousness.
But what if it didn't?
I find it more believable that the rare and dangerous X-Kryptonite did only one of those things (above), and the other thing just "happened" because of other alien tech, or the nature of a kryptonian consciousness.
Considering we saw that kid get powers at the kegger, and it had nothing to do with alien tech or Kryptonian consciousnesses, I think X-Kryptonite is about the powers.
Which means...
The eradicator can put a Kryptonian soul into any one on the planet, effortlessly, but it's just a person from Krypton, who has no special abilities.
Who the hell needs that?
Pishaw.
Tal-RoH wanted an army of gods.
Even if that god body became so unstable, that it couldn't safely maintain a transferred consciousness for long.
Was he losing Kryptonian souls every time he put souls (digital patterns, whatever) into a failed transfer, and the soldier didn't become superkryptonian? Or was he willing to let the weak die? Or was he actively killing his brothers and sisters he did not live up to expectations? I gotta assume that there was still original templates inside the eradicator, no matter how many copies he made of every Kryptonian, and cocked up the imprint? So he could run though a few copies of the same dude before he got something useful?
Same science that made Doomsday.