Ben Reilly was a clone, not a multi-verse Spider-Man.
Regardless, there's a reason why for a long time it was mainly just comics (and some side games like Shattered Dimensions) that had any sort of focus on multi-verse stuff: because the mainline series was running out of ideas and they let the artists/writers come up with some alternative ideas to do something more creative. It was never intended to replace the main/original timeline, just be sort of a creative spin. The Ultimate comics were the biggest example of this.
The problem I personally have is now how literally every adaption of Spider-Man has Miles shoehorned in. If it was just the animated movies and nothing else, ok fine, those movies are trying to expose lesser known Spider-Man variants. But the PS4 game, and now even the next MCU movie allegedly having Miles in, as well as basically every new Marvel show and game, it really does feel like Peter's 50+ years as being his own, loner Spider-Man have been completely retconned. Having two Spider-Men already kind of downplays the entire point of Spider-Man's existance, which was to be a loner type superhero who is hiding his fears and personal problems from his enemies. Having another one for him to confide in kind of ruins the whole point in that and it dramatically reduces a lot of the stakes knowing Peter just has backup at any moment. Or if its using the Ultimate adaption where Miles's is Peter's replacement (due to him dying), thats fine when its the basis of the plot, like Into the Spider-Verse, but I absolutely would not like it in something like the PS4 games.
I think the first PS4 game actually did a very good job with Peter, and I'm perfectly fine with Miles being Spider-Man as well, but I cannot help but feel like the story will end up being a lot less interesting when Peter doesn't have nearly as much pressure from being on his own. Theres still a lot of interesting Spidey stories that would make for awesome video games that are now basically never going to get covered if Miles (or even worse, Spider-Gwen) just keeps getting shoved into everything because he's somewhat popular from the movies.
It's funny how you see it as being shoehorned in, but when I ask my nephew who his favorite character is, he says Spider-Man and when I ask for clarification, he makes it clear that his Spider-Man is Miles Morales, not Peter Parker.
Saying Miles is shoehorned into stories, is like saying Robin is shoehorned into Batman stories, but you never hear that...
50 years? Spider-Man was introduced in 1962. Ben Reilly was introduced in 1975 (13 years later). Miguel O'Hara was introduced in 1992 (17 years later). Miles Morales was introduced in 2011 and has become one of the most popular comic book characters in the world.
The idea that they wouldn't use him is a bit absurd.
Can you name a comic book character more popular than Miles Morales created in the last 30 years? But apparently, he is being shoehorned in. Honestly, that is laughable. And it's not just because he is Spider-Man. There have been many characters to take on mantles that flat out fail. Most of them do.
It's not just the movie that has done well, but so has his game. It makes 1000 percent sense to bring him into the MCU and as for shoehorning, they built that out from the very start with Spider-Man Homecoming showing Aaron Davis and mentioning his nephew.
There are a lot of Spider-Man stories to tell, and him mentoring Miles Morales is just as valid as Batman mentoring Dick Grayson (1940), Jason Todd (1983), Tim Drake (1989), and Damian Wayne (1987). Note, that I've never once heard ANYONE suggest these characters were shoehorned in.