Cannot remove the cassette even with the right tools

[OakLeaf]

It should take a lot of effort to open and close the QR. You don't want it coming open spontaneously, or easily when you brush up against something. The rule I usually hear is that closing the QR should leave a mark on your hand.

Loose bearing assemblies need to be kept in adjustment and re-greased periodically. Generally, the cheaper the assembly, the poorer the tolerances it was built to, and the more fiddling it's going to need. It's definitely possible they were over-tightened at the factory, but it's a lot more likely that the locknut came loose over time. How many miles on the hubs? How many years (years would only matter if it's getting up over 5-ish; most grease will degrade over time, but slowly). Did they have a lot of miles in heavy rain, or is it possible you or someone else washed the bike with pressurized water and got water into the hubs?

I would expect the mfr would want the whole wheels back to see for themselves the type of damage to the cones (pitting, scoring, something else) and also whether the cups were also damaged. And also, as you say, because if it's going to be a warranty claim, the LBS doesn't want the mfr claiming that you disassembled it and overtightened it yourself.