Tools needed to cut your studs accurately : free running nuts that spin on by hand ( extra lug nuts ) , an air operated 90° cut off whiz wheel 19,500+ RPM , a sanding disk adapter for your cut off wheel with 120 grit disk , a Die that fits your studs .
Install your spacer with lug nuts torque to specs and mark your studs with a marker one full thread below the edge of the spacer , remove the spacer and install a free run nut to the previously marked line one thread below the surface , now use the nut as a guide to squarely cut off the stud then back it off halfway then back on , now with the sanding disk lightly sand the end of the stud nice and smooth , again using the nut as a guide . Now remove the nut and install the Die to clean up the threads ( a litle antisieze may help) clean the threads until the Die can be installed and removed by hand . Finally install a good or new lug nut by hand .
Do not get in a hurry , this will take a bit of time , now install the spacer torqued to specs and use a straight edge to ensure the studs are not protruding above the spacer !
There is Nothing wrong with spacers as long as they are properly installed . I highly recommend ( even though it's a pain ) to torque check the nuts retaining your spacers multiple times ie... 200 miles 500 miles and 1000 miles post install . Again every 6000 mile rotation or whenever you rotate your tires and anytime you have a tire off for any reason .
By all means follow the spacer manufacturers recommendations .