To use the TEI approach you need to believe in transcription. It is impossible for a transcription to reproduce the original object; it is always a selection of features from that object: the words but not their size on the page or the depth of the chisel marks, major changes in type style but not variations in the ink’s darkness from page to page or over time. Features that seem essential for a particular transcription can be encoded; what’s impossible is notating everything. And it may be that the creation of a digital description of a feature has little value for analysis: what you really want may just be the opportunity to see an image of the original, if the limitations of digital images are less damaging in your case than the limitations of transcription. A transcription might be regarded more as an index of words in page images than as a reasonable working representation of the text in works intended as mixtures of words and images and in very complex draft manuscripts where the sequence of text or inscription is difficult to make.