I think this comes with practice. I used to have a problem going the other way around (OTB was clearer than the computer screen!) but with time, they got equally comfortable in terms of board vision / visualization. I'd start playing more OTB until you start getting comfortable / over this visualization hump. Practice tactics with a board and a book (no computers). There is no such thing as a waste of time if you are trying to build up your fundamentals!
Your last point about tactics possibly being a waste for OTB experience is completely unfounded. Tactics practice helps you keep your pieces safe and find ways to make your opponent's pieces unsafe. This has no bearing on whether you can see the board in 3D or 2D.
I began learning tactics on chess.com and my rating is hovering around 1200. I am beginning to grasp some of the positions but I am grasping these more while playing online. However I feel that I don't or can't see these postions well playing OTB. I guess I would have to take each tactic and use a real board to visually see it. But this could be time consuming. Anyone have the same problems. I would like to hear from higher rated players as well to know how I can improve this. I know many say learn tactics...tactics....and more tactics but could it be a waste of time for OTB experience ?