I would say yes... Don't know where the hell Alisson is, cause she doesn't seem to be in the same to timeline or whatever the whole team are. Since I believe in this, I believe that the Ben who is with them is the original one from the Umbrella Academy, and not the Sparrow Academy Version. Although it may sound a bit wierd cause he acted like "normal"...

In my opinion, she merged the two timelines and everything is what everyone wanted for themselves, like an universal happy ending...