I think you will find its common on most MX5’s
I have owned two MK1s a MK3 and a MK3.5 and they have all had the same noise when idling as you describe which disappears when the clutch pedal is depressed, I assume it is probably the thrust bearing.
I have never bothered investigating the noise on my cars and done many miles in them, the noise never got any worse and the cars never let me down.