Have our worktops been fitted wrong?
You should have fixed the walls before they put up the counter tops up.  I understand the company's frustration with your set up.

However the real frustration should have been with the sales person or the person taking the measurements.  They should have noticed this and discussed possible solutions during the initial phase.

The fabricators/installers were basically screwed and the installers made the situation worse.  First I am sure your contract talks about an overhang.  Having a consistent overhang is part of any countertop installation.  This should be fixed.

However I do not think them scribing the entire back of the counter to fit your curvy wall is normal.  Again they missed this.  You are paying for a service and part of that is them being able to measure things.  (If no one came out to your house and you just sent in measurements though my opinion reverses)  

If you just have drywall above countertops there is a solution... If it works in your kitchen you can.  Have them install counters with an consistent overhang.  Then you could add another layer of drywall -thickness determined on how much you need to notch in your worst spot (and you can notch existing drywall too).  Then you will cover drywall notch with backsplash.  If they gave you some 6 inch pieces of your counter material it would probably look great.

On the other issues... The 90 degree thing - tops don't need to be at 90 they need to match cabinets.  So again worry about the overhang consistency.  On the joins - they should be sanded properly.  There should be no ridge.  It would be normal to have a very small amount of filler.  The really good companies make it almost seamless and the bad ones have huge joins.

Focus on the front of the countertops.  Make sure they line up the same with all cabinets.  Mention that you will let them notch into your existing wall - help them out and give them options.  If they can scribe one straight line in the back - that might be an option too and combining that with notching might work without additional drywall.  Also I would really ask them about a matching backsplash since tiling might not cover a wide gap in the back.