Yeah, Ben agreed to appear in The Flash once he was allowed to make certain changes he wanted for his character, apart from that part, Ben liked the overall script.
Director Andy Muschietti did make some changes in the original script after watching (and liking ZSJL), i doubt they are going to erase MoS BvS and JL form continuity.
Also, the production designer and vfx supervisor (Dj Desjardin) who worked with Zack on BvS and ZSJL are working in this (Flash) movie, he said he joined the crew after liking the direction they have decided to go for this movie.
Keaton also liked the script, which convinced him to return as Batman again.
I believe the movie's script is closely guarded and don't think anyone (apart from crew actually working on this) have seen the rough cut.