Anton: not at all, many marginalia are pen trials.
Rene: the shoddy paint job is a problem of its own. If the MS (or copy) was commissioned to be sent somewhere, then time constraints might explain the roughness. If, as VViews holds, the colors are not original, then they are irrelevant to this question.
The lack of ruling is not an issue. In 1406, Chortasmenos was commissioned by one monk Nathanael from the Prodromos Petra monastery to restore the famed Juliana Anicia Codex. Part of this restoration involved a transcription of the original Greek Uncial, which resulted in one of the most Voynich-like layouts I've found.
It all depends on the specifications of the commission, the amount of freedom of the scribe(s), their background, training, personal preferences, time and financial constraints and so on.