Difference between being able to fit and actually being part of the main timeline. The R movie is essentially a remake of the Makai Tree arc (confirmed by the director) and the S movie is based on a Christmas side story from the manga.
Besides that in the R movie Usagi and Mamoru apparently met 10 years before the series even though episode 1 was their first meeting. And nobody even brings up Fiore’s resemblance to the Makai aliens as if the events didn’t happen in the movie’s timeline . There’s also no reference to the events of the movie in episode 89 which essentially served as a recap of the series so far as well as a sneak peak of S.
And I know people handwaved that after the Viluy episode the Guardian Senshi and the Outer Senshi met a truce but they honestly act much chummier in the movie than theu did at the Viluy movie. Plus there’s no mention of Hotaru at all someone Chibi Usa was incredibly worried about during the time of the series that fans have suggested the movie took place in relation to
I think those are rather silly statements to try and get it decanonized.
For one the R Movie isn't a remake but it is a movie inspired by the Makai Tree arc. If it is a remake because it has similar plots to the Makai Tree arc and thus non canon then so too is The Force Awakens for Star Wars as it is just a New Hope except worse.
Likewise for the R movie again they met as children. They may not necessarily remember each other at that point when the first met. You meet alot of people as kids that you may not remember in the moment as you grow up only to meet them later and perhaps you don't remember that first meeting. Usagi and Mamoru were insanely young when they met. They could have forgotten that meeting since it was a one time thing only to later on remember this later.
As for Fiore I don't see why Fiore's resemblance to the Makai Tree aliens not being brought up is a reason to decanonize it. There are plently of characters in Sailor Moon who are essentially spitting images of other characters but people don't bring up their resemblances. Hikaru Sorano aka Minako's best friend looks exactly alike Ami just with black hair and green eyes. Hell Umino has basically three clones of him in the series. Minako's friend Gurikazu Amano and Chibiusa's friend Gurio Sorano. Yeah the little nerd boy in Chibiusa's class who looks just like Umino and acts like him is literally named Gurio Sorano the same first name of Umino and yet Chibiusa dosen't mention at all that said little boy is practically a clone of that nerdy boy that hangs around both Usagi and the other one around Minako. Hell in the Sailor V manga Minako's father is basically a twin of Usagi's dad Kenji. They look exactly alike and yet Minako never mentions this to Usagi. I mean Usagi and Minako's dad's look identical to the point they could literally be twins separated at birth who never knew one another not to mention Umino's clones either. It could be that either they didn't think to mention his resemblance to Al and En or thought about it off screen because again quite a few people in Sailor Moon are clones both in how they look and the way they act on Sailor Moon and no one mentions it. Plus the movie is obviously canon to Sailor Moon R because Usagi has her Crystal Star brooch and her Cutie Moon Rod which she got in the Makai Tree Arc. I mean if you want to be pedantic you could make more of a case about Sailor Moon S not being canon to the first two seasons as in the Makai Tree arc Luna said that only Usagi could use the Disguise Pen and yet in Sailor Moon S on the episode where Kaolinite is defeated for the first time Minako is able to use it to transform into the fake Sailor Moon. That is a rather larger plot hole then them not thinking to ask about Fiore's resemblance to Al and En or Usagi and Mamoru forgetting that they met each other when they were insanely young as many people do. I mean there were some people trying to say that the Makai Tree arc was retconned out of canon in the 90s anime simply because it wasn't mentioned in the Sailor Moon SuperS TV special when Usagi and Chibiusa were recapping their adventures in the series. They only talked about them battling The Dark Kingdom, The Black Moon Clan and the Death Busters with no mention being made of the Makai Tree or Al and En and I think we all know how silly that is.
Likewise for the S movie the Outers and the Inners could act chummy even when they had beef with one another. Besides they didn't really interact much until the big battles happened so they could be nice to one another in that instance. Likewise Chibiusa I am sure could be worried about Hotaru but she is also trying to live on witrh her life and keep positive. I think there was even this one point in S where she tried to fake she was ok after Hotaru's disappearance when she wasn't. So I am sure she is still upset with Hotaru's disappearance as say Usagi was with Mamoru's disappearance in the first season and they both showed moments of depression but they also weren't in total depression all of the time because they were trying to live their life and keep carrying on.
. Well you can always find explanations like : maybe they re just surprised to see her in stars because she told them after the super s events that she was going for good In the future lol 
