Because no one answered my question I selected one of the comment as "the" answer. Thanks mkl!
You can store data private to your application in PDFs, e.g. logo size and location in the case at hand (cf. this answer on PieceInfo structures). I would, therefore, recommend that you create the PDFs without the logo but store the size and location for a logo in such a PieceInfo dictionary. If adding a logo is required later-on, use that information to properly place the logo