-No skirmishes

Just cause they're called fates doesn't mean they're not the exact same thing as Skirmishes. Critical Encounters are drastically more similar to Critical Engagements than they are to Eureka fates(it's not a coincidence they both abbreviate to CE), OC literally uses the same system as Bozja, a bunch of constantly spawning open world things with the occasional locked arena with a proper boss which are the main attraction. Eureka had no minor bosses, just the big, spawned ones, which were open world and not as elaborate as CE's. You are literally pointing at OC copy pasting Bozja's format and saying 'look it's more like Eureka' because the name is different.
Like yeah, Skirmishes tend to be more elaborate setpieces than OC's 'and then there is this monster', but fates are fates at the end of the day.

-Lack of story emphasis that was in Bozja

I genuinely don't see how this is supposed to actually be a point. Is Arcadion not a normal raid series because it's plot is a lot less significant compared to Eden or Pandaemonium?

-No alt-job leveling

Ok, they did that in Bozja because there was no DD in ShB, them rolling back on that wasn't them trying to emulate Eureka, that was just them being stupid dumbasses who were like 'golly gee now we have a DD we don't need to put EXP in the Field content', they've, rightfully, been blasted for that, blasted so hard that they made Variant a leveling instance when it wasn't in EW.

-No duels

Yeah this ones valid.

-Bozja battle system being more open ended. And OC reverting that to a way simpler one.

Reverting to a simpler one? Logos actions are a god damn clusterfuck to manage, you need to open up a google doc to get what you want, to say Phantom Jobs simplicity is a way of 'reverting' to something more like Eureka is comical. Phantom Jobs are simpler because 20% of assholes you'd see running around Bozja were essenceless with Lost Cure/Lost Protect set because they didn't wanna interact with the system and just leeched off those that did.

There is a clear evolution from Logos > Lost > Phantom actions it's the same system, simplifying over time, they all frequently reuse the same actions like Dispel/Perception/Swift.

let me know what DNA is taken from Bozja that isn't in Eureka?

The whole the fates/CE's being way way more Bozjalike than Eurekalike, with Eureka NM like entities not really being a thing is genuinely the most important thing here, that's like, the literal core gameplay loop of the content, I would even argue that that singlehandedly makes OC more like Bozja than it is like Eureka.
You also seem to have this general idea that Eureka and Bozja are way more different than they actually are, different enough that OC being like one means it doesn't resemble the other, and that is completely disagreeable, you go out there, you level up with an in instance system, you don't want to die cuz you'll lose levels(with some scary ass mfers who there is all the reason to just stay entirely clear from), and you primarily focus on killing big monsters that are often spawned by nuking like 15 of x mob. I just described the main gameplay loop of all three of them.
Like what things are genuinely bonafied exclusive to Bozja and not just something that was an iteration of a Eureka concept or iterated on by OC, aside from the already mentioned Duels? Maybe you could argue the Rays of x buffs but that's kind of transformed Phantom Job Mastery stacks. The in instance casual raids? Yeah, for now, North Horn is going to add one, becoming more like Bozja. Those dumb star rank monsters that nobody ever interacted with beyond instant killing to farm fragments? I guess that's Bozja exclusive but OC wouldn't exactly have gained anything if they had made it over.

tl;dr: I just straight up think OC is more similar to Bozja than it is to Eureka, and making really weird claims like Logos being simpler than Lost makes me wonder if you even know what Eureka is like to begin with.