Doing metrology on production parts normally means disassembling them and putting them under the microscope or X-raying them, but sometimes there are problems that only manifest when the pen is assembled and closed. There's a lot of geometry that isn't visible externally in a pen, more so in certain markers. The writing systems are very sensitive to manufacturing tolerances, and out of spec parts are perceived by users as a bad pen or marker (which we don't want). With a normal X-ray, it is very difficult to resolve internal geometry deep in the assembled pen with any degree of accuracy.

CT scans allow us to examine internal geometry non-destructively and they are relatively fast to run. The scans shown in that blog post I would guess took about 6-8 hours of scanning + 1 hour of reconstruction to generate. Once you start the machine, it's completely automated from there, so you don't need a technician or an engineer sitting at the X-ray machine (which BTW is running Windows XP or something worse) takings images of parts.