Some good points you have risen here.
It does of course depend on the flautist. Even the particular instrument can affect how it project - headjoint cuts with more resistance project better in the lower register, and ones with less resistance tend to have clearer high notes. (Don't worry about that though - I was just showing how it can vary so much)
Flutes and Oboes a third apart are common. However, owing to factors such as the particular register that it is in, this will sound best if both are divided. Woodwind players are well versed in playing in unison with different instruments, and it can really utilise the different tones throughout each instrument.
Indeed I was. I have seen you mention it in a couple of posts and I thought it might be nice for you to emulate the scoring a little bit.
1. Yes, flautists will dislike a 4th Octave E. However, it's no worse than asking a piccolo player to play the top C - it's almost impossible to play.
2. Good idea, it's good to have these doubled. It makes it sound fuller as well.
Alternative suggestions:
You could simply have these as full tutti chords spanning a range similar to the arpeggio here.
Or, you could have the arpeggio being dropped down an octave at some points. This would take the high range off.