This sounds like a totally comprehensible argument for me. But the decision to stack chests is not based on asthetical reasons. It follows practical needs: In a PVP-base you want to limit the space where your valuable things are because you need the other space for fortifications (for example: gates, thralls, fake rooms).
Another reason for stacking is the advantage of having walls of chests in front of you to better organize your belongings (think of old pharmacies or a repository). This could, of course, be achieved with the “shelf trick”, but walls are not always available and as droch-aon already mentioned, shelves have a low hp.
I really love chests (as you can see in my screenshot :)) , but my problem with them in the first place is not that they don´t stack neatly. This makes for a (sometimes) vivid, organical view. The problem is that it takes forever to put one on top the other, because the placement is so limited, and I don´t understand the reason for that. In a perfect CE universe, WE should be able to decide HOW we want to put our chests