There is a ton of misinformation, miscommunication, and flat out not understanding about this 90 day thing. Sadly, the really amazing awesome stuff I have access to I cannot share thanks to a fuck-ton of NDAs and friendships that I won't jeopardize.
The rovers were not designed for 90 days. CONGRESS FUNDED THE MISSION FOR NINETY DAYS ON THE SURFACE So, lets take a step back for a second and talk about funding. NASA puts out a call for missions. NASA then runs feasibility studies on the proposals and decides if a mission will advance the goals of the Decadal Survey. If a mission will vastly forward the tech that can then be used in multiple other missions, that adds to the proposals (MER tech is still in use on Mars; the InSIGHT lander is made from MER spare parts). NASA then goes to Congress and begs for money. Building the machines happens on earth and creates jobs, increases our ability to manufacture high end tech and in general is liked by the people writing the checks. Assuming the mission is approved, the machine in question is built. In all of these missions, the most expensive parts are the support on the ground over the length of the mission, then depending on what is being built and how cutting edge it is, testing the built machine, then launch costs, then the manufacturing of the gear. To make the costs less, they say "90 days on the surface" as it is a way to cut the original costs on the mission. (Example given? Testing the James Webb Telescope is now more expensive than building the components and integrating them. Then again, JWST is pushing tech's boundaries HARD and they want this thing to last 20-25 years like Hubble.) The machine itself is built to withstand everything that the universe can throw at it. It has to survive the launch, the trip to wherever it is going, the landing/orbit and then the radiation and environmental situation once it is where it is supposed to be.
The machine itself is built with the best parts and tech they can get their hands on because the machine itself is NOT where all the money is going to go over the lifetime of the mission. IN the lifetime costs of Spirit and Opportunity, from what I have seem publicly listed, the Delta II for each rover cost $65 Million, each rover itself was $55 million out of a total expenditure of roughly $820 million, with an additional $120-$130million or so in mission extensions. Since the actual hardware is a low percent of the total mission costs, why not over engineer it? Why not plan for the thing to last a decade in the event you can extend the mission, because lets face it, paying to extend a mission is a factor of ten less than starting over from zero and building new gear. Cassini at Saturn, for example, was funded for four years. The orbiter was fueled in such a way at launch with Plutonium and thruster fuel as if they were going to fly for a decade or even longer. Fuel costs on these things comes out to a rounding error and is by far the least expensive part of the whole package.
Example of how this works: The Lucy mission. They are officially funding the spacecraft to end in 2033. They have several possible mission extensions and plans in the works that assuming the spacecraft is healthy, they can then pick several additional targets and do some more work. So the spacecraft is being built for a "12 year mission" in the official funding and legislation. But the people building and testing the craft have their eyes on much more.