can I cook a pork tenderloin and butt in the same roaster at the same time from raw, or should they be cooked in different pans until done?

I would definitely not cook them together - not for cross-contamination reason, but because each cut of pork requires a much different cooking method. Pork butt (shoulder) needs to be braised for a very long time so the connective tissues can break down, resulting in a tender finished dish. Pork tenderloin starts off tender, as the name suggests - cooking tenderloins is a very quick process (over cooking will cause it to become dry and tough).

If I were you, I'd cook the butt ahead of time and reheat when the tenderloin is done. By the way, be sure you're not thinking a tenderloin is the same thing as a pork loin. A pork tenderloin weighs 1 to 1.5 pounds, while a pork loin can weigh 3-5 pounds on average.

I know you said you have a special rub that you want to put on each cut of pork, but I'm going to post links to my blog just so you can see the difference in cooking methods for each of the cuts you're making.

Pork Butt (aka shoulder)
http://butteryum.blogspot.com/2009/11/old-fashioned-pork-roast.html

Pork Tenderloin (pictured below)
http://butteryum.blogspot.com/2010/06/pork-tenderloin-medallions-with-black.html

and just for the heck of it, here's a link for a pork loin (not tenderloin)
http://butteryum.blogspot.com/2009/08/maple-brined-pork-loin.html

Cross-contamination won't be an issue for you because they are cuts from the same animal. But if you're short on oven space, you'll want to be prepared to remove the tenderloin long before the butt finishes its nice long braise.

I vote no. Tenderloin is very lean & skinny in shape, and butt is quite fatty & thicker in shape. I worry your tenderloin will get tough even with your braising method. I primarily like to cook the butt until the collagen has broken down and I can shred the meat for pulled pork. I like the tenderloin to be just barely pink in the center so it's nice and juicy.

I am worried about putting them together due to cross contamination.

I am seasoning the same, with dry rub, then putting in cider vinegar, root beer and later bbq sauce. I thought putting together would help keep the tenderloin from drying out quickly.

I don't see why not, but the tenderloin is likely to get done sooner than the butt. Are you seasoning them identically?