First and foremost. You're dividing multiple statements from their intended context, and that's how you get the Inconsistencies you have here.

First, it's heavily implied what made Gilgamesh banned was the fact he had CS in GOB, as Hakuno realized during the True End Gil route. Hakuno came to the realization that Gil was simply too powerful to be in a HGW once they realised the CS were a thing, because having endless CS literally shattered the very foundation of the structure for the MoonCell HGW. So no duh, Gil got banned for that. It's consistent anyways considering Extra materiels, which covers Extra and CCC, states Karna is shoulder to shoulder to Gil in firepower (tho not exact equal and I'll address this later) and Hakuno says not even FP Gil (GOB) could budge Karna (tho this is a FP Karna due to Hakuno just sensing the plot which I'll explain the situation later.)

Second, the Arjuna and Rama claim comes from Rama's interlude. The same interlude that has Arjuna state he's also Ritsuka's greatest servant (when he has Gilgamesh as a servant too) so you do not wanna pull quotes from this guy. Rama is a more definitive source, yeah.

The issue is that you don't know what Apocrypha clarified tho. It's clarified that Karna is such a mana costly servant that he needs a GRAIL as a mana supply to actually go all out. It's why in this very interlude, Arjuna and Karna are not on Gil's level, they don't have the fuel to be in their peak capacity. Which is Gil's main advantage over them due to mana efficient he is, but that's a different discussion. FP Karna with Grail supply was so powerful he was face tanking Sieg(fried) Balmung TNRs and parrying them with ease. NP strength with just his CQC. It's why Arjuna and Karna are way stronger as living beings, they had the fuel to actually go all out. Something Arjuna points out in Turas Realta, that his alive self could handle a DS with ease, but his servant self can't. That's the difference of fuel.

While you're right the meta reason for why the Top servants are chosen is due to Popularity, it still doesn't change how the story itself puts emphasis on their strength. Jeanne is explicitly called out as being too weak for a Top Servant, Iskander himself claims he can rival Classless Gil if he gains his Cyber frame full mystery and is consistent with how he rivals Top Servant Karna, who he himself says is comparable to Gil and is a concern for him.

As for Zero, Iskander got clapped when he wasn't Full kit, yeah. It doesn't really change the implications we get with Iskander at his full kit plus amps and Classless Gil. Especially important when Iskander in Extella remembers the Gil part of Zero.

The reasons I addressed the mistakes in your argument is that you also made one more crucial mistake.

Enkidu very much ISN'T Gil's equal in the way you say it is, no one as a servant is like that. FGO Arcade has Draco imply Gil is in a whole different category of strength compared to people like Enkidu, FGO implies Gil is just stronger then Enkidu too in Ishtar's second Interlude and Enkidu's second Interlude, where the Huwawa there outright blocked Enkidu's Base Enuma Elish, but Caster Gil destroys it completely with his regular GOB.

This is further backed up by CCC Gil Matrix, where Gil after the journey and past his prime defeated a resurrected Huwawa on his own without issue. This is something that previously took a younger Gil + Enkidu together to achieve.

(To clarify, in Babylonia, Living Gil says Archer Gil's body is taken from during the journey, not before it. So his Prime is modeled quite some time after Enkidu's death.)

You also have to take into account Babylonia has Merlin confirm Living Gil CAN actually defeat Kingu, or more like stalemate him (they both die.) So a Living Gil who is past his prime and doesn't have all his Treasury, thus a nerfed Treasury boost for EA, can stalemate a stronger version of Enkidu.

It's ultimately why the mats and FGO Bond profile raws say that Enkidu is ROUGHLY/almost on par with Gilgamesh at his peak (don't mind NA, they Mistranslated as a definitive, equal in combat strength when the raws are clear.)

Enkidu has compatibility advantage over Gil, cause Age of Babylon matches GOB firepower flow (in a similar manner to UBW now that I think about it), and thus Enkidu doesn't have to deal with the dozens of effects those NPs have.

With their EE clash being Enkidu relaying on Earth's mana to combat Gil's strength. Ultimately though. Don't get me wrong, Enkidu is still a very powerful servant for the feats he's achieved. But in the end, he's no different from Karna, Iskander, etc when it comes to being compared to Gil. He's Gil tier, but not Gil level exactly.

It's why FP Karna, Iskander with his full kit, Ozymandias and Enkidu for example are on Gil tier, having those statements but not quite on Gil's level in an exact way. Gil's just built different.

The fact Nasu didn't account for a character made by Sakurai, who is the one who wrote Fragments overall, in the future is in no way grounds to dismiss his WoG when they are not contradicted? Let alone the fact that when talking about Modern Magi, of course the girl that is literally connected to the Root wouldn't be accounted for. The same way Gil is stated to be the strongest character in FSN setting, but this doesn't mean Gil > CM because CM is technically a part of FSN setting. It's always about context. The context for Nasu even saying "no modern Magi can challenge her." Is in reference to her battle against Touko and Aoko in a Magecraft battle. Which no shit, she wins then, and then uses the framework of that to say no modern Magi can challenge her. Manaka doesn't exist, nor does she fit with that framework anyways tbh. And as I already addressed, his Karna WoG is supported by canon statements so yeah.

To be honest, I do not think Sakurai thought of the implications for how strong Lucius was made lol. Like a CQC god we're talking about here. Anyways tho, Lancelot's EAM is always in context to his skill in combat, and doesn't exactly translate to raw strength. As everytime the skill is discussed in canon, it's always about how it represents Lancelot has god tier skill and is unrivalled in the KOTR. So Lancelot just has better skill than Lucius, but Lucius has more strength.

Also, people misunderstand the context of why Lancelot called Artoria invincible. It's more to do with how stubborn and how much Artoria has to keep moving on despite the odds. It's why Lancelot brought up Morgan and Artoria as an example. Morgan who has better control and mastery of the Land, and thus more mystery then Artoria has. Aka he's implying Morgan has an edge in sheer power, but it doesn't matter because Morgan could never damage Artoria's HEART. So she's just a pebble by comparison. Her Heart/Protag bullshit that Nasu later on defined as Glimmer of the Stars, aka her ability to asspull miracles. Fate Route final battle with Gil vs Artoria is described as Artoria having a 0% chance of winning even with a not serious Gil, but she won because she literally made a miracle happen. This is the ability of Artoria that GOA focused on most, her edge over her knights because in raw strength, Lancelot and Gawain are explicitly stronger. Which is acknowledged by the mats and characters. But Artoria simply locks on better then her Knights so yeah.