Thanks a lot for the further replies.
The consensus seems to be that there is little or nothing to worry about in this case.
If I’m OCD enough in the future to still be bothered by the misalignment, the best remedies seem to be to either fit a reduced-length leadscrew spacer, as Hopper suggests, or produce three new washers for the relevant shaft on the banjo: one a plain washer to go between the big gear and the small, and the other two C-shaped washers, the first to extend the unthreaded portion of the shaft so the hex nut doesn’t tighten down on to the gear itself, and the second to replace the factory C washer, which will be too thick to fit in what will be a reduced gap between the unthreaded and threaded portions of the shaft.
Just to clarify, the lathe came with no loose washers of any kind behind or between any of the gears so any misalignment is not caused by washers of a certain thickness being fitted in the wrong place.