Ruminations on post-Fall of Cadia/Gathering Storm and Primaris Marines 40K

Been wanting to post this for a looooooooooong time, especially after reading the gathering Storm lore/rule books.

I have read the trilogy, and the White Dwarf bunker extra fluff, and am sadly disappointed.
I was hoping - wringing my hands even - that there would be some friction between the ret-conned Primaris and Roboute against the rest of the Imperium.
Especially, as in the third book, Roboute thinks on his Father's vision and hopes for humanity, (ya know, that smallish goal Roboute lived for in WH30K) and decided to push ALL OF THIS TO THE BACK OF HIS MIND AS SECONDARY! WTF, GW. I was truly hoping there would be an open schism between the all-too-false religious juggernaut that is the Eclessiarchy (side note, I do LOVE the tragic irony that the Imperial Faith is based on Lorgar's writing). Was really thinking Roboute would have pushed the issue on his Father never wanting to be deified, since for Roboute only a day has passed, no 10K years.... He could have convinced Celestine that she is a psychic manifestation of The Big E, not a saint, and it sounded like there were no SoBs (that's Sisters of Battle, ya filthy blighters) left on Macragge to contend this claim, and Greyfax is a contrived nobody that GW created to sell more crap, so there's no need to even bother with her/it. Cawl is a ret-conned creation in direct connection with the Primaris, so being a project in the works for 10K FRiKKIN YEARS, one would think the Primaris would have been instilled with Roboute's beliefs, not the beliefs of the 'modern' Imperium, especially since until heretofore Cawl has been secluded working on Roboute's secret ret-con project of True-Scale Marines, not out learning about modern trends on your Rachel Ray-imperium channel.

But no.

Now there's a Primaris Chaplain (really!?!?!) According to what I've read, the Primaris are, like, totally down with the Imperial Faith yo. Very disappointed.

Ok I could use some feedback on this: just finished Rise of the Primarch (Gather Storm book III). I was under the impression that in the Gathering Storm(GS) books Chaos actually makes it to the Imperial palace, and Guilliman has to fight them off with his ultra-super-secret-double-probation True Scale Marines....
But, there's no mention, only some vague fluffy thing where Cawl makes it to one of the gates into the Throne Room, has a binaric chat with Tech Other Guy, and they leave 'to finish their work'.
I also though the Eternity Gate was the ONLY way in to the Throne Room, and was guarded by frikkin Warlord Titans.....................but GS III makes it sound like there's multiple entrances, which makes no sense, since it's supposed to the THE most secure place in all of the Imperium.

Really disappointed that there was zero detailing of Guilliman's conversation withe Big E, and, IIRC, Cypher somehow made it in to the Throne Room and had his own conversation with the Emperor as well. <-- Am I nuts? Does anyone else remember this?

So at what point in the books/lore is it revealed that Guilliman had this heretofore unknown (even to Guilliman, in the GS books, and the HH books, and any other book) Magos working on a secret project for 10K years, and when are the Primaris 'revealed' to be part of 30K-40K lore all along?