The top nut of a threaded headset needs to engage the steerer by enough threads to allow proper tightening. The spacer between the top nut and the threaded bearing cone/cup is usually just thick enough to achieve the top nut's tightening need. If too big a spacer is installed the top nut will not have enough threads to tighten on or allow a high enough torque (without stripping the threads).

The bar height is a function of the stem and not the steerer. The stem needs a minimal amount left in the steerer to be safe (usually around 2.5") and the bottom of the stem should be below the threaded portion of the steerer. There should be a bit of vertical range (of the stem in the steerer). But for higher bar heights then what the stock stem allows for the stem needs to be replaced with a taller or more highly angled one.

This is not the area to fudge things. Under braking there is a lot of force on the handlebars. Have you ever seen the results of sudden failure of the stem/bars? I have. Andy.