This might not be the answer, but for reference here is a problem that can occur if the plumbing is not installed properly.
If you look at Fig. 3, this is what a proper drain looks like. You'll notice the orange line represents the water level in the system, the water levels out in the trap preventing sewer gases from entering the sink drain.
In Fig. 1, you can see what will happen if the drain line has to go up before meeting the main drain line. Again the orange line represents the water level in the system, and as you can see the water level is much higher in the drain.
Fig. 2 shows what could happen if the sink was installed lower than the rise in the drain line. The water would never fully drain from the sink, since it would require extra pressure in the system to push the water up the drain.
![enter image description here](https://i.stack.imgur.com/Ws9y4.png)
I wouldn't guess this is the issue in this case; since as you can see, if you opened the trap in this case you would have more water drain than what is typically in the trap.
In a perfect world Fig.1 and 2 would never pass inspection, but as we all know not all plumbing is properly installed and/or inspected. So this could possibly be the case in this situation (given the plumbing was installed by an amateur plumber), but it is doubtful. It would be more likely caused by a clog in the line.
WTF is right! So the uneven sink drain is caused by porcelain chunks? If so they can be smoothed or leveled with a stone bit chucked into a drill. I'm unsure why the drain manufacturer doesn't want putty used with the drain? Putty is a neutral and mild sealer with no abrasive nor corrosive properties. Unless they give a specific reason for not using it, I would suggest it is your only option to make the new drain work. Perhaps that is what the white ring in photo #2 is for; an attempt to smooth and level the uneven drain opening. If it is solid it's epoxy. I see clear silicone in the photos; this must have given someone a headache in the past .
Best Answer
That doesn't make sense, but I guess it doesn't have to make sense to be a problem. If you're sure that you didn't drop anything down the drain, I'd try a plunger. The way to use it is not to ram it down hard, trying to power any obstruction through. Rather make many small strokes up and down to break the obstruction up with oscillations. If you think you did drop something in the drain take the trap apart and get it out.