I've been meaning to play through these pieces for a while, thanks for the reminder!
I just had a quick read / play through, here are some thoughts:
1. These chords / arpeggios are there to highlight certain intervals which are relevant to the piece as a guide to your ear to make sure you're tuned up well. They are just variations on Am(9) and E7, the I and V, tonic and dominant, of the piece. These fingerings seem chosen to highlight the open B in the Am chord, which can sound out of place if it isn't tuned well. So it has more to do with the key than the specific fingerings, they're just a good way to check those intervals across the neck.
2. A few thoughts here - the piece is based around quite a well defined rhythmic style which I'd definitely want to maintain throughout. So when I'm slowing down / speeding up I want the pulse to come along with me rather than just wander off. In terms of how much / how quickly to change tempo while keeping things sounding natural I'd focus on phrasing the melody in a way that comes naturally. It helps to sing the melody, at least in your head, and get a feel for the tempo changes in relation to the melody first. If your tempo change is part of a musical phrase it will help to avoid sounding 'heavy handed'. I did a quick search of recordings online, found a chap called Norbert Neunzling who I think does a good job of maintaining the rhythm and phrasing throughout (thanks Norbert if you're out there!)