Ruby Quest/WMG

The Dummy is connected to Chzo
Either an Avatar or another servant.

Think about it, a group of people suffering horrible and painful mutations, going insane, suffering endless agony that not even death can release them from? That is totally the god of pain's MO. Also, Ruby's third eye created by her mutation leads to what is practically Chzo's Catch Phrase, "it hurts", when used too much.

Tom is channelling Odin
The deity has of course been dead for centuries, the final speck of his divine essence being cast into the depths of the ocean by Christians, unable to destroy him entirely. It was an incredible coincidence that another, even more ancient and even more dead god was buried into the exact same spot.

When the hospital was built in this place as well - much less of a coincidence, might I add - both entities saw there an opportunity to escape. While the older god took immediate action with its dreams and medicines, Odin, his presence much smaller and weaker, only nudged things along here and there, trying to orchestrate his own freedom while keeping the other god safely hidden in the depths. He needed to find a champion. A vessel for his might. He found Subject 6, the one we know as Tom.

Despite being large and manly, Tom was also a shy and polite person in heart, and this is exactly what Odin desired: he had no use for mindless brutes, after all. He granted Tom his greatest gift, the Berserker Rage, very rarely and very occasionally, during the year he spent down there: Tom put this strength into good use every time he got it, for most of the time just trying to protect his sweetheart Ruby.

Tom was locked away not because he was a danger to anyone in itself, but simply because he was the only resident of the facility who could ever match Ace in a direct confrontation. But even so, Odin managed to manipulate Ace into removing Tom's right eye and cast it into the black abyss below the hospital - exactly how Odin had done to his own eye, so very long time ago. He was the one responsible for poisoning the fish, for locking Tom away for three full days: those three days of agony were his metaphorical Tree of Life, where Odin himself spent the same time crucified immediately after discarding his eye. This ritual was all it needed for the deity to transfer his full essence to Tom, essentially making him a physical god.

The older, nameless god saw this, and first sent Ace to destroy Tom in a desperate attempt to stop Odin, and when that failed, sought to possess Ace entirely in order to finish the job itself.

Conclusion: Allowing Stitches to rescue Tom was fine and good, but by doing that, we missed out a mighty confrontation between gods. Such a shame.

GLORY AND FAME; BLOOD IS OUR NAME; SOULS FULL OF THUNDER; HEARTS OF STEEL

Red did actually come back once.
This isn't really so much wild mass guessing as it is a logical conclusion, one that went unstated at least in the Fur Affinity flash version.

When Stitches comes back to life, Red, who killed Ruby a few days prior, realizes that Ruby will return as well, and tries to avoid the problem by offing himself. He figured since he hadn't taken the medication, he would simply die and get away. I think he succeeded; he did successfully kill himself on that day. However, he did not know that Ace, under Filbert's orders, was lacing his food with the medication, resulting in his revival.

Because he only died once, as opposed to the several other times Ruby and Tom did, any mutations he may have were probably at best minor and, if anything and assuming the mutations are related to the injuries the patients had before, was most likely that ridiculously toothy laugh. Because he only died once, it's likely the mutation did not have much of a chance to recur and build like the others.

The "medication" was actually powdered Cosmic Horror.
It's the only thing that the outside world doesn't have, and they did seem to be studying the heart used to open the locker. Its amazing regenerative capabilities would seem ideal for testing on live subjects, and it did seem to work. At first.
 * Is it really a WMG if it's blatantly obvious?

The "cure" requires a death by violent trauma to really kick in. Or at least, just violent trauma.
Hence why the euthanized subject didn't come back, where everyone else did. She died peacefully, from her systems shutting down, as opposed to the body having to regenerate tissues, like Red's cheek or Tom the cat's... everything.
 * Subject 2 had been off the treatment for quite a while when Filbert euthanized her. That was the whole point: see how long after they were taken off the treatment the revivification would work.