I know this thread is a little old, but I’ve opened an issue on GitHub for it convertTilemapLayer for isometric tilemaps not setting bodies properly · Issue #5764 · photonstorm/phaser · GitHub
I think I might also have a solution for it, so thanks everyone here for the investigative work. Turns out that getting the x value in getBounds() just wasn’t supported for any kind of projection that isn’t Orthogonal.