I experienced similar discomfort with my first e-ink reader Kindle Touch back in 2011.
I ended up “calibrating” my expectations of a footnote tap:
1) Try to tap with your finger in such a way that when actually tap the footnote, your finger covers the footnote completely. I know it sounds strange, but then I just got used to it.
2) The thing is that iPhones and tablets predict very well and calibrate this difference between “where is that thing that we see on the screen” and “where we actually tap to get this thing”. This is especially true for iPhone’s
keyboard.
eReaders, as far as I can see, lack this calibration.