It's important to make something very clear - the Z4M gearbox is a noisy box by design. There are many cars that are misdiagnosed as having "loose input shafts" and noisy input shaft gears. I have yet to see a Z4M gearbox that has come out, stripped down and have signs of anything other than normal wear.
Dealers get it wrong, mechanics get it wrong. Without seeing your gearbox, it is impossible to comment other than there are many box changes made without good reason.
In any case, the gearbox is an individual outsourced unit which is not related to any other component in the car. You may even have the benefit that they changed the clutch at the time for good measure.
Don't let the gearbox replacement worry you.