I've been using reversals for over four decades now, but my approach to them has shifted considerably, from a simple black-or-white perspective to one that encompasses a wide range of subtle shades. I don't see them as primarily negative, just "different," less a matter of altered content than one of skewed delivery. I like them because they expand my interpretive palette considerably and create avenues of inquiry that might otherwise remain unexplored. I use them with almost all decks (but not with TdM because I still don't have a solid grasp of it in the upright condition). If there is a psychological element to tarot (something I don't entirely accept) I think one place it resides is in the concept of reversal. Regarding Elemental Dignities, I use those and reversals both; the former mainly tweak the relative strength or weakness of the focus card, while the latter can shift its angle of attack. As long as everything is kept coherent and systematic, I can see no reason to limit myself. I also agree that the spread positions add their own emphasis.
As to how the cards "get reversed," the first time I thoroughly randomize a new deck, I make sure to turn some of the cards as I work through the process. I've been using Grizabella's "four pile" method, but recently I saw someone using seven piles, so I started doing that; it's easy to just flip some of the sub-packs when gathering the deck up. Then I do a normal shuffle. I repeat those steps to a less rigorous extent between readings, but don't pay much attention to reversing the cards other than that. Since I seldom read for myself now, I let my sitters do whatever they want when shuffling and cutting the deck.