Two things I haven't really seen either side of the current debate really process are Joe's capabilities and Joe's experiences.
For Joe, literally everything he makes is something that'd be a central figure in some kind of myth. That is the scale he works at at a baseline now, if I recall the WoG rightly. I saw someone try to disprove Star Trek scanners being used earlier, but really, with the sort of stuff Joe has, he could probably get an atomic scan of everything in a million mile radius without issue. The issue is hiding the fact he did it, something that brings me swiftly into my next point.
Tinkers are bullshit. Hell, capes in general are bullshit in their areas of specialization. And the Slaughterhouse 9 is not made of chumps. Joe's still trying to crack Bakuda's Deadman Switch at this very moment, and when you consider the sort of timeframe Joe operates on, the fact it's held up this long is downright ridiculous.
Joe's scale is downright mythological in nature and Bakuda's still hanging in there. THIS is Joe's impression of the average Tinker. Not Iron Man armor or whatever. Attacks worthy of designation as a WMD, shat out casually from half-scrapped projects and soda cans that have demanded response with proportional force.
I don't think it'd be unfair to say that the code for it has to be at least like, half pure power construct from the shard, to focus back on that. Given how Tinker shards in general work, as per Wildbow's explanations of them being essentially Elder Shards that have run out of easy ways to test their abilities and effectively choose to take a totemic route to express this wide variety of abilities through pretending to make devices that express the actual effect, I don't think anyone can really conceptualize the sheer potential depth or breadth with full confidence. Hell, I can't help but feel our boy Joe got a bit shafted on getting his own Tinker power, when put into context like that. Just because the Worm doc is playing by 'understandable technology' rules doesn't mean actual Tinkers are. Kinda puts into perspective how WH40k tech was needed to figure out this stuff initially, given the upper level of how exotic it can get. They're used to the Warp's fuckery.
Tinkers are bullshit and Joe's had experience finding out exactly how bullshit they are, without even necessarily knowing the outstanding factors or having a solid baseline to compare the extreme end to. Joe sees Bonesaw and Mannequin, and sees two capes that outstrip Bakuda and Leet, who were effectively nobodies and bad jokes before everything that happened. Admittedly, he ain't far off, either, given Jack's Thinker/Master power putting them in places where they'd be most effective for his own sake. But while we can say something along the lines of, 'Oh, it's fine, they aren't actually that dangerous by comparison,' not only is that coming from a place of ignorance as to what their capabilities when going up against Apeiron will be, Joe's even more in the dark and off-balance.
Now, Joe's confident about the fight anyways, for good reason. He's cracking the Deadman's Switch. He's gotten overhauls for tons of stuff. He's at the point where very little threatens him, but he's not the kind of person who's going to jump the gun because of confidence alone. Pride Mantra has probably taken something of a toll on him, there, but he's got about a day or two to be sure he's not about to walk into an improbable deathtrap, which goes by a lot faster and a lot slower for him than us, and explicitly only in ways that benefit him. For all he knew at the start of this chapter, the Siberian could telefrag him before his armor got a chance to pop off. Even if she doesn't punch through Life Fibers, there's a lot of meat that she could probably scratch.
Even minor brain damage would be a major difficulty tweak for him, under cover of some unprecedented stealth effect, or his scans could've been detected by some nebulously defined Tinker device or Crawler sense if he went for the high fidelity and resulted in the Slaughterhouse 9 running for their lives under threat of Tungsten Chimpanzee, meaning a delay in his execution of them while he's stuck in the persona he has until he gets something that lets him just do whatever. I'm decently aware of how improbable this actually is, but for Joe, the chance is big enough to be a real concern. Hell, no investigation as to what's up and he wouldn't even figure out Manton's a thing. He seemingly takes out the Siberian through, let's say Spiral or something, only for her to pop up in another city three weeks later. No reason for Joe to pursue a civilian vehicle that he might not even be paying attention to - It's Dinah's Amber Alert all over again.
Remember, he doesn't know what Jack's power is, either, other than it's been subtle and opened up a staggering amount of opportunities for the S9. Inference would indicate some kind of probability manipulation or coincidence-creation, something like Shamrock's power. And since we're talking probability here, well, the odds of something like the Unholy Hour happening were slim, but not none. It happened, and he's not about to take a risk like that when annihilators and such are involved, and... Oh, hey, look, they've got a Siberian.
Only tangentially related to this, but there's another point I'd like to bring up. In this story, even simple or outright self-destructive powers can reveal immense hidden depths. That's what this story was supposed to be about, if I recall Lord's word correctly. Experience also matters quite a bit, when these powers come up. I don't think it'd be an exaggeration to say that if everyone stopped envisioning every single power as a single superpower but rather as somewhere between a thousand and a quadrillion minor powers all coming together to make one central power/powerset, it'd probably help everyone with the scaling. Tinker shards, probably towards the higher end of this, given the variety of things they're supposed to test and they should be old.
Overall, I think everyone's made some good points, and while I can't really make up what side I'm on fully, whether it'd be better for Joe to wait for them to walk just a little too far and make a show of them or just execute them with all the fanfare of making a completely normal sandwich, what I will say is, I find it really weird that Joe's got any difficulty finding anything on the planet. He doesn't need superpower scans to detect something as weirdly shaped as Crawler. Or Mannequin. Or Shatterbird's dress. Or Murder Rat. The list goes on. It's only not a SoD breaker by merit of Joe trying to keep as light a touch as possible, thus probably using tech from like, a week ago. It's the little things, y'know?