Okay, let's break this down.
Just for the record, I use Magic Coat with Earthquake, so everything I'm going to say next assumes that
Groudon: Dragon Tail is rare in general now. You may be able to catch it on Roar, but it's much better to attack Groudon and get phazed anyway if they have Dragon Tail anyway. If it did have D-tail, it won't do that much. Incidentally, Lum Berry has the worst chance of beating Groudon, when Extreme Speed is only netting you a 3HKO at +2. Really, the best options for Lum and Magic Coat Ekiller against Groudon is like same, and Lum hits Groudon for way less. Silk Scarf has a chance of 2HKOing after Stealth Rock and Life Orb a better chance still, two items that really appreciate Magic Coat's ability to keep you away from Toxic without having to decrease your reliance on Lum. What status can Groudon do to Ekiller that it really hates anyway? Toxic still means Groudon's dead and Arceus has a few turns of a killing spree and Thunder Wave is the one which Arceus least dislikes. On the other hand, Lum Berry means Groudon can phaze you at least twice.
Giratina-A: Yes, I guess it could have Dragon Tail, but if you catch it with Magic Coat with WoW, it is seriously doing practically nothing to you the next turn (and who does expect Magic Coat anyway). Funnily enough, even with Lum, Giratina will get the burn on you because it's not like Shadow Claw 2HKOes even at +2. I'll give you Shadow Force, but SF EKiller is really easy to play around and is arguably harder to use than Magic Coat.
Giratina-O: Again, I concede this one, but 1) it's not that common these days and 2) you might even be able bounce WoW in its face and laugh at it anyway. On the other hand, if I were using Giratina-O, I'd probably Dragon Tail Ekiller out first anyway, and Shadow Claw can't OHKO it, certainly with Lum.
Rockceus: Yes, Lum is overall more reliable against Rockceus, but it's not like you always have to be in the mindset "Ekiller must sweep or else". Arceus is not Xerneas that's got one chance to sweep and that's it. You can bounce back WoW and then switch out to something else easily. I know you can tell me "well Rockceus has forced Ekiller out and it's won", and I would say "...so what?" Why can't you recognise that there are times that Arceus will have to switch out? You can beat Rockceus with Lum, sure, but by running Lum Berry you'd arguably to a list of other Pokemon that are arguably a lot more dangerous than Rock Arceus, which I'll list later.
Bronzong: I'll concede this one, but like Giratina-O, it's not that common.
Ghostceus: Actually, if Ghostceus had Focus Blast, it beats you anyway if you're not running max Speed (which is the kind of spread that Lum and Magic Coat is better for) if Focus Blast hits twice, regardless of whether you had Shadow Claw or Magic Coat. It outspeeds you and 2HKOes you. On the other hand, both Lum Berry and Magic Coat beat Will-O-Wisp versions, so it's not really something that's important.
Gengar: You beat Mega Gengar with Earthquake anyway. I know it can choose to not transform and attack you in its normal form, but that would mean your opponent knows you're carrying Magic Coat. Seriously, how many people do you think would be able to tell? I guess in tournament games if you've stalked someone you could guess that, but then you can just switch it up with Shadow Claw / Force if you think they'll predict Magic Coat. It IS slashed last, so Shadow Claw and Force are still going to be the vast majority of Ekillers, so what makes you think that people would deliberately take the small chance that Magic Coat is there to lose against the majority of users who use Shadow Claw? Also, if just the mere presence of Magic Coat on the set makes people not transform their Gengars to take down a potential Magic Coat Ekiller (remember untransformed Gengar cannot outspeed a Jolly Ekiller, which is very much on the cards), then that alone warrants a slot to throw your opponents into that hesitation.
Okay, you wanted to know what phazers that Magic Coat Arceus beats:
Lugia you've mentioned already
Skarmory is one Pokemon that normally completely walls Ekiller that gets completely wrecked by Magic Coat. Yes, he can keep spamming Toxic, but Magic Coat has more PP than Toxic. So, you either end up Whirlwinding him out or you bounce back some Spikes. Either way, you get the winning end of the deal. On the other hand, unless you're using Overheat, you're losing to Skarmory with 3 attacks, and if you ARE using Overheat, you're losing important coverage for other stuff.
Giratina-A I've gone through already
Support Arceus that use Roar - With Lum Berry Arceus being relatively common, people can Roar out Ekiller if they really can't afford to risk Ekiller being Lum and potentially losing. Magic Coat would not only bounce out WoW, but any Arceus potentially using Roar, the most common first responses to Ekiller (because seriously, who is going to start off attacking Ekiller with Judgement, unless you're low on health anyway?)
Groudon with Roar - Yes, I am aware that Groudon can just EQ you, but again, like support Arceus, if the guy is using support Groudon, who's going to EQ your Ekiller when it's that much safer to Roar you out instead? If you catch it with Magic Coat and for some reason that Groudon comes in later, it has to make the choice whether it wants to get reverse phazed again, or use Earthquake against you and then lose because you 2HKO it with Extreme Speed? Against 3 attacks, it's a pretty easy choice for the Groudon, they just click Roar.
There are also a couple of other small niches for Magic Coat as well. You serve as a really good anti-lead with it. This is like the one time where I like leading with Ekiller, because you can bounce back Taunt/SR/Spikes/Sticky Web/Spore from all those anti-leads like Deo-S and Smeargle and automatically seize the momentum. I've had so many Deo-S's get Taunt thrown back in its face and they have to back pedal immediately.
Anyway, the point of Magic Coat is so Arceus is less vulnerable to status when it's using LO or Silk Scarf. I know you love Lum, but there are crucial KOes you miss with Lum Berry against very crucial threats. Mega Mewtwo X is the biggest one. With Lum, you fail to OHKO it, and in return you get OHKOed by Low Kick. With Silk Scarf, enabled because you now have Magic Coat to deflect status, you score a clear OHKO against it after SR if it transformed that very turn (so it took 12.5% as regular Mewtwo and transformed in that turn). You score an easy OHKO on offensive Yveltal after SR with Silk Scarf, while with Lum, this is not guaranteed (which means you could potentially take a massive hit from Focus Blast or Dark Pulse, something you might not be able to afford after getting hurt when setting up. You have a >50% chance to OHKO Scarf Zekrom with Silk Scarf boosted ES after SR while you're not doing that with Lum. Seriously, you're not even guaranteed an OHKO on Palkia without SR while Silk Scarf will do it every time. This sort of thing gets pretty common, which is the reason I never liked using Lum Ekiller, even when I was really keen on using when I was theorymonning Ekiller a long time ago. The lack of power from Lum is something I really don't like, and Magic Coat gives you a form of protection not only against status while keeping the power of Silk Scarf/LO, but also phazing.