Hi Adrian, just to share my experience, when I have studied this pieces honestly I have never concentrated on the duration of the inner voice but instead on the execution of the melody. As long as the melody is fluent and "legato" the accompaniment is coming along and sounds good.
As far as the duration of the bi-chords, you are necessarily forced to play them with the semiquaver rest in correspondence with position shifts (impossible to do make the bi-chords play longer when you are passing in the melody from the G to A and from B to C#).
Anyway, this is a transcription of a beautiful piece for piano. In the adaptation for guitar the piece is getting a different character, it is normally played slower compared to the piano version, it is normally played with a more cadenced tempo and gets a very similar mood, in the first part, of the Capricho Arabe. The piano version is for sure normally more fluent and more elegant/sophisticated. I would concentrate in trying to give to the pieces authenticity. Remember that, with our beautifull instrument, it happens "very rarely" that what is written in the partiture is going to played "exactly" by the guitar.