Your method of using 2 indicators on the rod at the same time will work great and assure you that it's right. KE's method is basically the same with moving the apron and will give the same results with 1 indicator.
Remember to bore your brake to final dimension (if not already done from the manufacturer) over bullet diameter (.020-.030) while it's on the rifle. Which will make your brake opening concentric with your dialed in bore and threads.
After your all done and before you pull it from the lathe, put your rangerod back in the bore through your brake. If all is done correctly, you will see your concentric clearance all around the rangerod through the brake. This will assure you the insurance that you will not have a baffle strike and the job is correct.
Don't know your level of experience fitting brakes, so please don't take this post as questioning your abilities, because it was not meant as so.
If you have any questions, feel free to give me a call and I would be more than happy to try and help over the phone. 734-848-4689
Edit** just realized your threading for a can, same principles apply except the rangerod will probably be to short for the check that i mentioned above. A gordy rod would work the same except it would need to be held in a drill chuck from the tailstock end. Assuming the lathe is in line..and of course you wouldn't need to do any machining on the can