I was quite pleased with that finale, mostly because I was really worried that it would turn out Fitz had been dead the entire time and I was going to flip some things if that turned out to be true.
IMO, they most definitely ended up in an alternate timeline when they ended their time loop in season 5. I like to pretend they ended up in the same one that was created when Loki stole the tesseract during the time heist. (I like to pretend that him doing that created a timeline where Thanos never got the tesseract and therefore didn't snap anyone in 2019, which is why no one on the show even mentions it.) But at the beginning of last season, Daisy said something about 5 years having passed so I think they were trying to keep the show lined up with the movies, even if they didn't cross paths with any MCU characters anymore.
Maybe Fitz brought them all back to their original original timeline (and they'll be shocked to find out about Thanos...) or their second original timeline. Regardless I wouldn't make much of a fuss about it if they used these characters in any MCU movies. Fury is "retired" as Director so there's no reason why Mac can't be the Director going forward. May could easily fit into the next Spider-man movie. And I personally would love it if after Falcon and Winter Soldier, Bucky left Sam to be Cap and joined Daisy and Daniel for a trip in space, something akin to the Man on the Wall comic. (And use Mark Hamil to play older, wiser Bucky...) There's also no reason Daisy and Carol Danvers can't meet up in space. And so on and so forth.
I'm also a a Babylon 5 fan and maybe it was just a coincidence but I thought it was funny that Fitz, Simmons, etc. were in the blue hazmat suits while interacting with their past selves. Which is exactly happened on B5 in the 4th season.