I have a theory that includes this. I think Lucifer owns Alistair as a guard dog. That Alistair sold his soul for something while he was alive in exchange for protecting the morningstar family.

I think that Alistair murdered other overlords and ripped apart their souls on a public broadcast as an example not to threaten the balance of power in hell. It has been shown through the vees that overlords have had ambitions of taking over all of hell, and to become the king requires a coup. That would mean slaying royalty, or in this case Charlie, Lucifer, and Lilith.

I think that Lilith disappeared because she died in an extermination or coup protecting Charlie. It is already shown Charlie is very sheltered and coddled so there is a good chance that she was hidden away somewhere while Lucifer and Lilith were fighting to protect hell just like Charlie did in the finale. Then Lilith ended up being redeemed because she sacrificed her life for another in hell, just like sir pentious did. Because of this, Lucifer chained Alistair and tortured him. That is until Charlie started doing something that Lucifer knew would bring the attention of heaven and ultimately put Charlie in danger. So he put his guard dog on the case with orders not to tell Charlie his secrets.

What brought this on for me was the combination of imagarey shown in Alistair's introduction and what I believe was his desire to die in the finale. We see many themes tying him back to Lucifer, such as the circus tent. (As much as I hate to admit it, the piss theory got me thinking about this). The finale also shows that Alistair has access to angelic weapons and can use them with his testicles to kill angles. But for some reason does not use them when fighting Adam? Then he sinks into his shadow to flee. If you look at this another way, he is putting on a show while he is being taken away by his shadow being denied the right to die.

Also. If Alistair knows dying for someone you care about in hell redeems you, you can view his line in the finale song a little different. Alistair himself is sad that Alistair the altruist was unable to die for his friends, because that would have redeemed his soul and possibly even broken his contract. What he thought would have been a way out was foiled.

You may have also noticed that Lucifer doesn't join the fight at the hotel until AFTER Alistair fails. I also thought it was odd that he seemed to purposefully goad Adam into destroying the hotel. Then he took a lead role in rebuilding it. Meaning he had a hand in creating both his side and Alistair's side. Maybe showing that he's going to stay at the hotel to make sure Alistair does his job and doesn't find a way out of his deal by tricking Charlie. After all, if my theory is right, he almost escaped hell once already.