Will is listed as "additional personnel" in The Mission credits. He was a major contributor to The Mission as he co-wrote almost every song with Tommy, played some instruments and produced the album. He is hired help

I'm fairly certain he only played certain tracks during The Mission live shows. They don't need him for the entire catalogue.
He was the vocal producer for Regeneration I and II, and was part of Tommy's The Great Divide album (co-producer, engineer, backing vocals and guitar on some songs)
Oh.. and if you didn't know, Tommy and Will actually prepared most of the album in secret, without telling anyone else in Styx.
"We kinda snuck around for a long time. ...The idea of me coming to everybody else and saying, 'Look, Will and I have an idea for us to do an album about a mission to Mars' wasn't something I could confidently go in and talk about. I think everybody might have been overhearing little playbacks and this and that and the other and they were getting curious. I'm sure there were some discussions on the bus when I wasn't around. There finally came a point where it was, 'Let's bring everybody in.'"
https://ultimateclassicrock.com/styx-mission-new-album/