Yes, the reason for the cap is to be cosmetically pleasing and to protect the threads a bit from corrosion. Allowing the nut to go further down would result in exposed fork threads above it, which are ugly anyway, and worse once they rust.

All you have to do is to cut the fork to the proper length, leaving a mm or so beneath the cap. If you want to allow for a possible larger stack in the future then just add some spacers under the locknut and cut the fork that much longer.