Don't worry, it's not physical vs digital, in fact it's physical AND digital all the way. Anki has been a life saver to learn JLPT and now JED (if you have android) has become my weapon of choice when I am reading. Which is one reason I wouldn't go digital on my purchases yet, I need the dictionary all the time, each page I can expect a word I never encountered yet (I am at that stage where I get this pleasant feeling of surprise when I've read 3 pages without looking up anything) and that can really trip you up. And for the dictionary digital is the way to go (at least as long as you have furigana).
As for the "feeling more real" aspect, I would not be too concerned, manga reads as well on a screen as on paper (but in english...). And don't be too happy about paper furigana, at time they can be barely legible. It just gets worst when digitalized, and I can't see them up the quality, nobody wants a 120mo epub.
Then again that is just one guy's opinion, I hope others contribute, there may be sites I do not know about etc. Also if you want first hand experience of digital manga, bookwalker has excerpts. Here is a common exemple of the way furigana gets unreadable when you zoom in: http://bookwalker.jp/de98b6c10f-d76a-4c2a-b42e-224075f91611/?sample=1