Meat doesn't really begin to take on smoke until the meat temps. are at about 100 degrees, so just heat to that point wouldn't make much difference. After that, it just depends on how much smoke flavor you want. If you begin with smoke and only go for 2 hours then switch to just heat you may not get much smoke flavor depending on the size and type of meat you're smoking.
The carcinogens could become a problem with heavy bark. This is basically burnt meat and is supposedly not good for you. But being people been eating this way for god knows how long I think you'll be ok. Because you are smoking food doesn't mean you have to have a heavy bark, some like it that way and some don't. It's up to you. Besides, it wouldn't be the first time these type of people were wrong!!!! Remember when they said eggs were bad for you or when that Oprah person said beef was bad for everyone???
I'll eat what makes me happy and live the way I want. No politically correct for me, ever!!!!!
Note
Clarification/Correction:
My statement at the beginning of my post may have been slightly off or misunderstood. It was brought to my attention and I wish to apologize for not conveying this concept correctly. Below is the correct wording and is more directed to larger cuts of meat. I hope this clarifies any misunderstanding.
Smoking:
Allow the shoulder to warm up to at least 100F internal temperature before you switch to the smoke setting. This will allow the meat fibers to open up, resulting in better smoke penetration.