I do feel like it’s very possible that part of the final comic is just coincidence or not even referring to G5 in anyway. And even if it was the intention, the FiM comics probably aren’t going to have anymore effect on G5 then they did the G4 show. It can be used for a basis of a headcanon being a sort of B-canon where it could be considered canon depending on the fan if nothing outright contradicts it, but probably is not going to be THE basis for what caused whatever happened, should that ever be explained in G5 proper.
Remember that Sombra remained evil throughout the show’s run. But was given a backstory and some kind of redemption in one arc of the comics. So it shouldn’t be guaranteed that the comics mean anything in regards to G5. I kinda doubt that the “Season 10” comic’s concept of multiple Elements of Harmony in each land outside of Equestria ever gets mentioned especially.
Hope “the element crazy” that Whitney had portrayed will disappear by itself as it is really meaningless - although the cunabulans`s heinous crimes against the world could explain why the realms lived apart from each other with a minimum of contact with each other. Whitney has left so many loose ends that one does not know where to start - or stop.
The only thing of value from S10 is at least the story of Pinkie and Cheese and the formation of “Friendship Empire” that we saw in the last page of the issue. This can be continued with zero problem in the G5, as the technological level revealed that a world community had existed when the magic disappeared. Whitney believed that the war between the cunabulans and the royal realms in the shadow of Discord’s chaos reign was what triggered self-imposed isolation of Equestria and other countries so that only trade, some travelers and low-ranking diplomacy were left.
This followed to disaster when Storm King launched his world conquest, the Abyssinians did not inform the others, the hippogriffs did not send a message about their fall. Celestia and Luna were completely blind to the threat from the south, which led to Twilight in S8 and S9 as S10 becoming preoccupied with the world outside Equestria.
But the images from where Everfree Forest once lay, and the fact that the Harmony Tree had lost its magic - unthinkable, even if a new “element war” were to occur - show that the threat may have come from within, from the very mysterious forest area. The deer civilization from the IDW comics may have been extinct when the entire valley was laid waste. I do not think anyone saw this coming. The deers have their own elements if we were to follow Whitney’s logic that all peoples throughout Equus have their own set of harmony elements latent in their magic.
And where did it come from? We know very little about the time before the great frost when the modern Equestria originated in the valley where Canterlot and Ponyville were located, probably around 1,500 to 1,600 years before S1. From Anugypt / Southern Equestria we know that the written history is at least 3,000 to 4,000 years old. It is very possible that G1 - or at least G4’s version of G1 - took place from between 4,000 to 2,000 years before S1. So much could have happened in such a long period, including a worldwide empire. We have only two possible examples, Empress Megan Williams`s Crystal Empire from a fanon reality and Emperor Grogar Empire that may have existed in the canon world of G4 and G5.
The best thing though is that Whitney`s Folly is ignored for posterity, the characters, the lore and the formation of the Friendship Empire can survive into the G5 lore as part of the historical background.