I've just tried this with my X-H1, in AF-C the camera always refocuses when pressing the shutter butter regardless of whether self timer in selected or not -
If I de-couple the shutter button focus in AF-C, holding AF-ON continuously focuses as you would expect, and the pressing the shutter does not cause a refocus - again as you would expect
In self timer mode, the X-H1 behaves as you describe, switching to AF-S (from AF-C) with the AF-ON button, and it also refocuses when I press the shutter button, so the de-couple has been disabled.
If I'm in manual then it focuses with AF-ON and does not refocus with the shutter button - I have AF ON in AF-S - (so not decoupled) - self timer ON/OFF makes no difference.
So why do you have to de-couple shutter button in AF-S when you are in manual??