I have to disagree....just random things that come into my mind that were altered in the comics to match the MCU.
1. The Scarlet Witch and Quicksilver are no longer mutants but a result of an experiment ( following the origin of the MCU).
2. Tony Stark has a arc reactor in the chest.
3. Hulk is a member of the Avengers ( funny enough Hulk is a founding member of the Avengers but left the group in .....number 2 - he did not last long lol) and he got back into the group in 2012 to match the release of the movie.
4. The area of the universe where Earth is located is no longer Badoon territory but Chi-Tauri's.
5. Red Wing is no longer a bird but a drone.
6. The Defenders are no longer Dr.Strange,Silver Surfer,Namor... ( the original setup) but the ones from the Defenders TV Show.
7. The Guardians of the Galaxy core is the one depicted in the movies ( original members post-Annihilation like Quasar,Nova Prime,MoonDragon,Phyla-Vell...go in and out but the ones that are always in the group are those).
8. Gamora turned from the edgy character , from the last of the Zen Woberi, the wielder of the Godslayer...ultimately the avatar of Death that even Ryder was afraid of ( while banging her) to the well intentioned warm character of the MCU.
9. The Infinity Gems now have the same color scheme as the MCU.
10. The Nova corps that got decimated in Annihilation popped back after GOTG Vol1.
11. "Wakanda forever" is a battle cry in... well Wakanda obviously.
12. Pepper Potts and Happy reappeared after decades of absence.
13. Nick Fury Jr ( Sam L.Jackson lookalike) got his way from the ,now non-existent, Ultimate Universe to E616.
14.Many...Many...Many!!! visual redesing of characters ( Falcon getting the MCU wings....Ant-Man getting the MCU suit)
....
So let's be precise about the bolded statements:
A. If you mean that the MCU does not affect the comics I can't disagree more....quite the opposite comics have become the laboratory of ideas for Marvel Studios ( mostly because one successful movie if the income of several years of comics). Exhibits presented before.
B. If you mean that E-199999 is not reflected in the comics this is not correct. There's several comics based in the E-199999 universe. This is the logo for
those series.
C. If you mean that E-616 and E-199999 have never interacted ( in the comics) I really don't know but I can't see how is this relevant...EarthX ( maybe the best alternate universe Marvel has ever done) never interacted with E616 either but they are both contained in the multiverse.
D. If you mean that E-616 and E-199999 have never interacted ( in the films) well...my theory (and I remark this term) is that movie E616 overlaps comic E616 ( it substitutes the other ) so if this what you are saying I would agree that never have and never will.