Sheath is too short! Can I finish in EMT?
Technically it would be a nipple and the code does allow for certain liberties in nipples such as larger fill requirements and no derating of conductors. I wouldn't call a short piece of SE "unsheathing to use as individual conductor". Also consider the alternative, which would be to splice say THWN to the SE. What would be worse? The small piece of SE extended or a splice where you have to leave accessible to maintain the splice, since splices are 80% of all electrical conductor problems. 

In short it's all a matter of following code to the letter or the actual intent of the code. Personally I would just as soon reduce the number of splices over any other alternative.