Just checking before I install the mod: My Consignment Store Clerk is an exact replica of a Sim I made and stored in the Bin for a a few hours, which I didn't find out until I had placed that Sim (and they were immediately attracted to one another...). Obviously I need to be rid of this doppelgänger and while I'd rather not install an entire mod for one incident, I don't know how else to fix it. Is there another way?

I believe the way this works is that it's StoryProgression (SP Population module) that governs where the genetics for sims spawned to take up those roles come from. Assuming you are using SP and have that module, on NRaas > SP > General Options > Options:Sims > Options:Immigration/Emigration > Replace Service Sims with Immigrants is that set to True? If so, you will have other options on that menu to Disallow Bin By House and set Chance of Bin Offspring to zero (if wanted) just as we can do for resident immigration under the Options:Lots menu.

Without SP Population, I think all bets might be off the table and just about anything can happen.

With Register, you can assign precisely the sims you want, wherever they happened to have come from, to the desired role objects. It also makes the assigned sims behave a lot better and, in my game, helps to stop the incessant spawning of hundreds of unnecessary homeless Role and Service Sims.

Depending on which consignment store. Without SP and/or Register the Consignment Shop from Ambitions will assign one of the unemployed residents failing that it'll randomly generate one in a day or 2 via immigration but with Register the Consignment will only use one of the homeless
The Elixir Consignment shop will always use one of the homeless

...but with Register the Consignment will only use one of the homeless

Register has a setting that governs whether assigned role sims are always to be pulled from the homeless pool or (if any are available) to automatically assign residents. Do these settings not work with the consignment registers?

NRaas > Register > Allow Immigration
NRaas > Register > Allow Resident Assignment

Only if there are no homeless available from what I've seen the Consignment store and the Elixir Consignment store are the first 2 roles 9/10 that Register fills
The game will probably never allow a resident to fill the Elixir Consignment store as that is a 24/7 role

But I've never let Register use residents though

Okay, I've changed the Bin immigration thing as igazor said, so hopefully it won't happen again, but how do I get rid of the guy who's there now? It was the Elixir Consignment Shop, but I have the mod set to remove homeless.

If it's SP set to remove homeless, that will happen pretty soon but it's difficult to pinpoint when. If it's Overwatch (different setting), it either happens upon the next startup or the next 3am run. But as he was never meant to exist, I would probably use MC to Totally Annihilate (TA) that one.

"But I've never let Register use residents though "
To be honest, neither have I though I do use Register to assign particular residents to particular roles myself. Or actually no, come to think of it, I move a homeless role sim or two into a house thereby making them residents. But sometimes I wonder where players get all these "spare" residents from.

Actually it will allow a resident at the regular Consignment store if you can pause the game fast enough I failed 2 times succeeded on the 3rd.
If it's the Elixir Consignment it was a pre-made homeless that was already there and roles sims are moved into the service houshold and protected from being removed.