Made a few comments but wanted to clarify on some of your questions.
For the marganali, what do you mean that they coincide with the text? Do you mean they are marginal revisions of/additions to the text rather than commentaries on the text? If so, you're right that we might not call them paratexts; they could just be scribal corrections?
There may or may not be reasoning behind which motifs are used for a given headpiece. Did any patterns stick out to you?
SMDL Link: https://sinaimanuscripts.library.ucla.edu/catalog/ark%3A%2F21198%2Fz196124r
Description Document: https://docs.google.com/document/d/1KRB4_vFzFko9MBfL7QAhjLR20OdYce-a/edit
Outline: https://docs.google.com/document/d/1wo8K-7zcMD-_Y08IOSiYHUTFpk9CHwnYF6zmnFyTdr4/edit
Summary: A prophetologion with numerous marginalia and decorative headpieces.