The simple cure would be to just change the nuts.
The factory nuts are kind of goofy anyway.
Use a 10x1.5 flanged nut with a 15mm hex. Most hardware supply companies will carry them. With these nuts, installed height has little or no effect. In fact if the studs are long enough you can thread them all the way into the case.
Grade 8 nuts
Material: Medium Carbon Steel, Heat Treated
Proof Load Strength: 150,000 psi min