I'm confused, are you cooking in a smaller smoker that doesn't have enough airflow to evenly cook the meat, or maybe your smoker doesn't heat evenly where maybe you have to rotate the meat for even cooking?
I can cook 1, 2, 6, or 8 pork butts of relatively similar size and they are all done evenly and at the same size.
I never cook to temperature, I only use the meat probe temperature as a guide as when to start checking for tenderness.
There is no single way to cook Pork Butt, find what works best for you.
I follow BluDawg's recommendation "You can not cook your pork butt/pork shoulder to a specific temperature and call it done!!!!" If you have a target temp you are doing it wrong: The goal of cooking a tough cut of meat is to make it tender, not make it hot. Therefore you should monitor how tender it is, not how hot it is.
There are a couple of ways to know when pork is done:
The first being the poke test; When you stick it with a thermometer, skewer, fork or whatever, and it goes in without little to no resistance like warm butter, it is done.
The second being the bone twist/pull test; When you firmly twist/pull on the bone and it wiggles like a loose tooth, then it is done.
The third being the tug test; When you have a boneless pork butt, grab a piece of meat with your thumb and index finger and you are able to pull a piece of meat off with minor resistance, it is done.
Pork butt is a very forgiving cut of meat due of the fat content and the amount of connective tissue it contains. If your pork is tough to pull then it wasn't completely done. If the pork simply falls apart when pulling, it is slightly overdone. Even when slightly under-cooked or slightly over-cooked the pulled pork will be great, however it will never match the taste and texture of perfectly done pork as indicated above.
Every piece of meat is different, and therefore each will cook differently in some manner. I have had many pork butts done as low as 185 degrees, while others do not indicate being done until they reach 200 degrees or more.
Because of this variance in temperatures, I usually start checking for being done when my internal probe says 180 degrees, after that I don't pay any attention to what the internal temperature is, except for personal reference. The bone is a much better predictor than temperature, simply put When the bone wiggles like a loose tooth it's done.
Again, your smoker might be different, so do what works best for you.