The cutout is because it's the only cover that I know right now that thought of the Dual Sim phones. I can imagine that the delayed they had when releasing the cover was because of this, the first pictures shown the cutout perfectly fit for the regular version, but then after the delay the pictures they began posting were always showing the cutout for the Dual. If you ask me it was a good move, that will assure them to fit in all versions of the phone, but for people like me with OCD issues, it can affect a little the appearance of it. One thing I don't get is that you mention that you need to be very careful when opening the flap, well, it doesn't matches the form of the flap perfectly, but it sure has enough clearance for both the sides and the flap opening slot.
Once of the reasons I sold my initial Z3 (Dual D6633) and looked for the D6603 was because I thought I was going to be out of luck when looking for a cover that fits it and I like the look, so seeing that they thought of that also it was good for me. The fact is that now it looks even better fitted on the D6633 than in the rest of models ad the cutouts fit perfectly, ironically.
The other cutout for the magnetic that bends, yes, that was the second thing I noticed as well but if you look very close to it, I can understand their design choice also, as it's the only way it can allow for Magnetic charging for everything on the market right now, Docking Chargers and the Cables and Adapters (Like the Magnector) that requires some clearance in that area, if not, you will need to be removing the cover to charge.
I've also noticed the water-like effect that can be seen, both times, it has been just after I've cleaned the phone with my Microfiber towel and Screen Liquid Solution, if the towel is not completely dry, when you put the cover back it creates that, so it seems that it's just humidity, so I just remove the cover and dries it and put back the cover and problem solved.
No product is perfect and you are right with your issues with it, but all in all, when you look at the reason behind the first 2 of your issues, it was a matter of design decision and I'm one that appreciates what they did, it can be recommended as the most complete and well thought cover for our Z3