It would be nice to have transclusion working in DT3 (part of the MMD 6), but this can be overcome by letting the files in an indexed folder and then using Multimarkdown Composer ou nvUltra to view them.
This seems to make writing longer essays in DT a task more feasible. As it is right now, you can’t properly view all the parts together if you can’t keep them in different files.
In Scrivener, Ulysses, Tinderbox or Connected Text this would be easy.