Bowportes

It didn't exactly "override" your manual shutter speed. The front dial is designed to get you those in-between shutter speeds that do not exist on the shutter speed dial, so it actually "fine-tunes" your chosen shutter speed, giving you greater precision of control. This is easily turned off in the menu so that it will never impact your shutter speed.

Actually, on the X-Pro3, a separate raw file is saved for each exposure of the multiple exposure. These could then be processed as raw files and layered to achieve the same multiple exposure that you get out of camera.