Plumbing sanity

If there is one thing that is essential when designing something intended to hold water (like a sink or a toilet cistern), it is that the holes in it (plug hole, and where the flush comes out) must be able to be sealed...right?

Typically, a seal is made by squashing a bit of rubber tight against a flat surface. 

So, why is it that:

 1. My new sink's hole for the drain does not have the top and the bottom of the hole parallel? That is, you put the drain in but and the nut + washer at the back are at an angle to the surface they are meant to make a seal with!

 2. My new toilet cistern does not have the base of the cistern at right angles to the back of the cistern....so that the flush mechanism fits wonky. If you make a good seal, the flush mechanism cannot align with the button on the lid of the cistern, or if you want the flush to align with the buttons, then you cannot have a good seal.

If these simple design details were right, then the fitting the appliances would have taken a fraction of the time it's taking me now. Surely, everyone who buys these items will have the same problem.

After a couple of false starts, the sink was not too bad: plenty of silicone instead of relying the rubber washer did the trick...but the WC is still a work-in-progress. I suspect that since I prefer the fail-safe (no leaks) over functionality (being able to flush),  I'll end up with something can can only do single-flush, not dual flush.

Do real plumbers have these issues...come on, what's the trick?