That's a very valid concern, JC.
At the typical hot smoking chamber temps for fresh meats of 225* and above, the meat's surface will be pasturized before the internal temp rises much at all. With non-intact meats, any process (deboning, injecting, stuffing with garlic, etc, mascerating/tenderizing) that
could have introduced harmful bacteria
into the meat is the real risk. While the surface is still the most likely place to find these harmful bacteria, they will be heated to temperatures above what they can survive before they can multiply and release enough waste toxins to be harmful for human consumption.
The center of the mass of the meat is where the internal temp and time guideline becomes the most critical, as the center mass will take the longest to pass through the danger-zone temp/time range (41-135*/4-hrs). If you can meet the guideline with center mass temp/time, the rest will obviously take less time, so measurements between the center mass and surface would not be necessary. It's all about
internal temps with non-intact fresh meats once they hit the cooking chamber.
Hope that bridges any gaps and clarifies things abit better for you. Bbally explained alot of this in the
low and slow discussion in the
food safety forum awhile back...
HERE's the link to that thread. Note: in this thread, you will see mention of the temp/time guideline of 40-140*, which was updated in 2009 to 41-135*...this thread is from 2008.
Eric