I'm very much a noob, but I had a similar problem with my player character. I had a collisionshape inside a collisionshape. Removing one of them resolved the problem where my player would be thrown away as soon as the scene started... Maybe the same is also happening for you?
#physicsbody3d car launches into space
woeful bluff
split gull
nope only 1 collision shape and the raycasts make an exception for the physicsbody so nothing like that should happen :)