General Lane has actually been refreshingly honest the entire series. I think we can definitely take him at his word on a lot of things. The only "lying" he has done has been to not volunteer information, which is
normal and proper military conduct. It's not malicious, it's part of the protect and defend method.
Lane really does regard Clark as a force for good, even if he gets exasperated with him at times. That's why they work together so often. When Lane says he stockpiled Kryptonite to protect Clark I think he means it - he doesn't want Superman taken out of the picture because Superman does so much good. On the other hand, it would be stupid for the military to NOT consider what would happen if Superman went rogue - for Og's sake, in our world the government has plans for alien invasions, role-plays the zombie apocalypse, and probably has a plan for what to do if the Girl Scouts go insane and try to take over the country. Consider hypothetical problems is part of what the Department of Defense does (whether or not it is done well is another question, but let's not go there...)
I wish they had made it more explicit, but Clark is a smart guy and I think he understands Lane's stance on this, which is why he doesn't push back. Clark is well aware of how overpowered he is compared to humans. If he wasn't before he certainly is now considering the effects of going rogue would be. It's hard to argue with the logic of Lane developing weapons to take on Kryptonians.
Apparently this iteration of Clark 'can't' just indefinitely hold his breath (or never breathe to begin with) the way some comics interpretations can as a gas he had to breathe worked (and a gas mask/rebreather/whatever worked to protect the Edge meta so it wasn't skin contact).
Re-watching that scene, the first blast of green gas catches Superman unaware, which is plausible give Rosetti's superspeed. Clark probably got a lungful, or part of one, before he realized what was going on and started to hold his breath (Clark says very little throughout the fight, so he might in fact be trying to hold his breath). The first inhalation impacted him, which might have made it harder to not breathe. Rosetti, once the mask it torn off, does a lot of gasping. If Clark is able to hold his breath, even part of the time, and Rosetti doesn't (or can't, because he's base human with meta powers, not base Kyrptonian) that goes a long way to explaining why Clark does as well as he does despite being affected by "synthetic Kryptonite". Too bad for Rosetti he just assumed Irons had run off. Irons is a baseline human with no powers who not only took on Kryptonians, but also
won on multiple occasions. He's a badass.
A gas that was meant to weaken Clark so 'more traditional methods would work' which does not necessarily mean lethal force. So even with the kryptonite that doesn't mean they were looking for ways to kill him.
Right - which shows again that Lane is not a bad guy. He really is looking for ways to deal with a threat, and not just "kill it!" but multiple methods. Look for some of these to be deployed against Edge's army. That's going to be a fight where Superman might very much need armed allies.
Mildly surprised Irons didn't build any anti-kryptonian weapons into his winnebago's internal defenses. Limited resources for those maybe? He had enough to set that trap for Clark last episode but we know very little about his this world resources (hell we know little about his home world resources) at either point in time.
I think it comes down to Irons having very limited resources - he tried to obtain more kryptonite, after all, but couldn't. He cannibalized his ship that he arrived in for parts for the "creepermobile". He just didn't have the bits he needed to set up anti-kryptonian defenses, and may be what he does have he uses for weapons rather than defense. He might have been more concerned about humans burglarizing his RV than about Kryptonians finding it - after all, Superman could juggle the whole thing if he wanted, or crumple it up like a wad of tinfoil. It's like bomb squads - against conventional explosives they wear those bulky suits and stuff, but squads practicing anti-nuke procedures don't bother with them as they won't protect them if things go bad and just get in the way of doing the primary job. No point in armoring against Superman if you don't have the resources to do so, as half-assed won't work and is just a waste of money and effort.
Papa Lane is not going to be happy with Clark's decision to let Irons go on his merry way
Maybe, maybe not. We don't know if Lane is aware of Irons going on his way, or if he is aware and maybe even backed the idea. Presumably, Irons was debriefed. Certainly, if you're looking to keep anti-Kryptonian deterrents around Irons is your man. As noted, he has taken on Kryptonians and
won. He may have lost the war on his homeworld but he survived it. IF Clark ever goes rogue Irons would be someone you'd want on your side.
I also assume Irons, for all that he appears to be taking a bit of a vacation at the end, will continue to investigate Edge and matters around his little crew. Irons might accept this world's Superman as a force for good (at least for now), but that doesn't mean he trusts anyone else.
I do find it significant at the end that Irons has the AI change the profile from "Captain Luthor" to "John Henry Irons". It signals that he is moving on from a past where absolutely everything was focused on killing Superman, revenge, and grief to resuming his identity as a full human being with the full range of emotions and concerns. He's not done with the grief process, but he is moving through it. Also symbolized by taking to the road again. I expect we won't see him again for a few episodes but I expect he will be back at some point.
I also like that they address Jonathan's issues with being non-powered in the family, and that Lois has started to talk to him about being un-powered but in the "orbit" of someone with powers, a situation she had lived with for decades. I would have preferred Clark to point out that Jonathan running into danger and needing saving is something that he, Clark, has had to deal with because not only was Lois doing that sort of stuff before they met, if anything it's gotten worse now that she knows Clark will bail her out. Not that she
deliberately does this (although in the comics she has been known to!), but she's a lot less cautious than she might be if Superman wasn't around to save her.
I think we've been teased a bit with whether or not Jonathan gets powers. I still think we've seen some glimpses, but that doesn't mean he'll even ramp up to where Jordan is. Or they could cop out and Jonathan could get exposed to x-kryptonite, but not have the side effects full humans do. Or maybe why part of why Jordan is getting powers is exposure to x-kryptonite, and he's just gotten a bigger dose somehow than Jonathan.