I can see players attempting to farm arcade for these danger rooms to pass their hall of heroes requirements, hence why you want to have small percentages for the higher drops. If those drops were bound it wouldn't be too big of a deal but it's just one more way to get around the system.

Lore-wise we have had a defector - we were sent to retrieve him and it didn't turn out too well. From what I can tell Spiral Knights are simply honor-based beings, and so defectors would have to have broken some honor code. Arkus didn't want to fight us, but since we would've taken him back to HQ by force, he stood his ground.

One thing to keep in mind is that the subtowns are friendly to Knights, but likely only the Spiral Order, seeing as how we have several knights stationed down at those depths. Rogue knights would have to acquire all things on their own.
Having specific scenario rooms is okay but still sorta eh.

Basically I guess my point is that encountering these knights is pretty much its own little battle that doesn't need to happen. It's kind of unimaginative and doesn't add anything interesting. I do sort of have a solution to this though.

Imagine if Three Rings worked a sort of NPC "rival squad" into the game. This would be a squad of knights led by another NPC knight who is highly competitive and wants to sort of prove themselves as being the best knight of the Spiral Order. While this knight isn't a bad knight themselves, they see all of your accomplishments and want to prove themselves. This knight will always reach the next rank up before you (outside of vanguard, they will forever be a champion), and will have a few missions added to the game where they either assist you, or compete against you.
The idea is that you have a healthy competition with this Knight who, over time, gathers a small squad of knights together. They will appear in various story missions, either helping you defeat a tough enemy ("Hey look who's here! Glad to see me?"), or being a sort of antagonist ("Well well well, who do we have here. You're after that treasure too huh? I guess we'll have to settle this the hard way!").

Early on, the knight starts as a single squad knight, believing they can take on anything. After reaching the snarbolax they realize they need a squad, and get another knight on their side. Royal Jelly adds a third, and Roarmulus Twins adds a fourth. Now to make this interesting, each member has a different role. The knight that is the anti-you is the squad leader, second member is a striker, third member a recon, fourth member a guardian. Each member has a different attack style, with the squad leader alternating between weapons.

Now while story mini-bosses are confined to the missions, this rival squad could actually be put into the clockworks as a random encounter. In stratum 1 it's just the squad leader, strata 2 and 3 squad leader + striker, stratum 4 squad leader + striker + recon, strata 5 and the full squad. Heck, for challenge's sake this enemy squad could even revive any downed knights in your party before engaging the fight because they're competitive, not brutal... Or, well, maybe they wouldn't fight you if one of your members was downed because that'd be breaking a knight's honor code.

This sort of encounter would make all parts of the game really stand-out and interesting, as you could run into this squad pretty much anywhere, and depending on where you run into them they either will make your life harder or easier.
Hell, perhaps they give you a usable item that summons their squad to assist you, with a few easter eggs depending on where you use it (eg. in a fight with them they pick up the receiver and just are all "??????, seriously?", in Haven they'd join you for a moment saying "Hi _______, here to he-.... Wait for real? No, I won't help you in your bid war, earn that money yourself!", in your guildhall they'd join and say "Hi ______, what's the-, oh for crying out loud... I mean I like what you did with the place but I've got skulls to crack", and in lockdown they're all "What the occa- oh #&%$ no I don't need my pride broken in front of a crowd"). Just something as simple as this rival squad would breathe a lot of personality into the game.

My idea was that rival squad encounters would be added to existing missions. For example, your first encounter with said Knight might be during the "toy soldiers" (3-1) mission, or the "faith in armor" (3-2) mission. The rival squad would be in your mission lobby for all of your boss encounters, warning you of the dangers ahead, but saying "don't worry, i'll take care of everything, just give me a few minutes to prepare".

Second mission encounter would be during the "chilled to the bone" (5-1) mission. Third encounter would be "axes of evil" (6-1) or "plan of attack" (6-1). Fourth would be "in cold blood" (7-2). Fifth would be "the vile engine" (8-2). Last encounter, at least rival-wise, would be "alone in the dark" (9-2). You would encounter their squad once again in the "It Came From Below" mission, however they would be trying to help the last living recon knight stay calm. They might say something like "this squad really was hit hard. You were able to take down Lord Vanaduke, eh _______? I say you go up ahead. We'll try to get these recons back to Haven safely".

Heck, it could open up the idea of something super creepy, like after you load into the unknown passage, they try to contact you via comlink to tell you not to go forwards; to come back, but the message is all scrambled and unintelligible. After you complete the 10-1 missions, the rival squad will be in the lab, and talk to you about how concerned they were to lose someone with such special talent such as yourself. From this point on, hell, you could even make these knights into a special vanguard vendor, or make them into some new and interesting idea for the endgame. Special bound accessories perhaps? Prestige store? Let your mind wander.

Bottom line is that this rival squad would be added into various missions as a way to break up the action, add a bit of attitude, but also to allow for minibosses in the arcade. The could be trudging through the arcade, spawn with some of the monsters in a room, and after clearing the room you can talk to them and they'll say something like "Hey, what do you say, want to test your might?" Heck, you could make some battles mandatory, like the loot box one I gave earlier.

This programming also opens up the idea for lockdown bots to replace players when a leaver happens. Two birds with one stone, eh?