There is only one reason only for injecting a probe later in the smoke, "Food Safety". Thus the intact muscle rule, that whatever pathogens or contaminates on the exterior surface of the meat are now pushed into the interior, and now require that your meat reach 140º+ in less than 4 hours "danger zone". However as soon as the surface of the meat achieves 140º to a dept of about 1/4", for 5 minutes, you can then insert your probe, this may only take a few minutes for the surface temp of the meat to hit 140º.
Note, all meat thermometers, the end should be placed in the thickest part of the meat, making sure the tip does not touch any bones. The only pocket to worry about internally might be a fat pocket, even then it should have little effect on the temp reading.
Otherwise there is no other reason to wait until later in a smoke to insert a probe, aside from some practical reasons that apply only to your situation.The following is my own application and may not be considered safe, only follow at your own risk, I am not encouraging anyone to follow my example.
I test my temp probe in boiling water, and then insert directly into the meat prior to putting the meat in the smoker. Personally I want to know exactly what is happening between the smoker and the meat temp. If the meat temp is rising too slow or too fast, then I will be checking closely the smoker temps. This gives me a chance to make adjustments during the first hour, if necessary. I wish I had 6 probes, I would have one in all large pieces of meat, so I could move the meat around according to the different temps of meat and spots inside the smoker. I keep a temp notes during the first 2-3 hours of the smoke, this helps me on those smokes where too many beers may result in doing something in error, plus there is no guess if the meat is cooking properly or not.
I recently had a pork roast with the internal meat temp rising really fast, I checked the smoker temp it was dead on. So I kept watching and at the end of 90 minutes, I decided I had to do something or the meat would be cooked but not tender. I dropped the cook temp 30º and opened the door of the smoker to dump the heat. The meat held temp for almost an extra 90-100 minutes, before I ramped up to the desired cook temp, the extra time holding temp and slow cooking did the trick and the pork roast was very very tender.
Note it has been recommended that an swap with alcohol be used where you intend to insert the probe in the meat. If your seriously concerned then by all means do it. I figure I will change my method as soon as I see BBQ competitions telling their contestants to either not use probes until yada yada, or to swap the meat. Apparently this is a non critical issue with even the largest BBQ contests, and they are run by people a lot smarter than me. We all know that 85% of the contestants do it.
, illness due to food contamination is no joke and should be taken seriously.
I have my opinion as to why I think whole meat cuts are safer. I edited out the comment about the fattie, I miss stated so I edited out that sentence...
If you have any questions please consult the USDA Kitchen Companion
, also consult SMF's stickies on Food Safety.