--B12 megadosing is designed to allow approximately 1-2% of the dose to be absorbed passively through the mucous membranes in the digestive system, and not necessarily in the intestines. This happens only when it is taken by itself, though--the cobalamin molecule is the largest one the body regularly used metabolically, and it is easy to block absoprtion of it if one takes B12 with something else (even other B vitamins). The cobalamin molecule simply cannot compete very well with other things at membranes.

This is usually enough to sustain people--in a 1000mcg dose it means around 10-20mcg will be absorbed, and since the daily requirement is thought to be 4-8 micrograms, that's generally enough. But it is possible that people with ongoing conditions may need more (part of the reason some do 5000mcg doses).

And, I suspect absorption is more difficult for people with problems in that realm to begin with, such as for celiacs. At Cornell Weill, the usual recommendation for people with gluten problems is to go with a daily, seperate dose of 2000mcg and up, and many do 5000mcg as long as they don't get too jazzed up (which can happen with those doses) until their malabsorptin issues subside. (Interestingly, one of the more reliable ways of determining THAT is measure of non-supplemented winter vitamin D level.)