So here is the thing about the capacitor and the fitting window…
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the fitting window is assuming that all modules will be “on” / “active”… so it will calculate how long your capacitor will last under that circumstance.
Generally speaking, you will not have all your modules on at the same time. So the time for the capacitor to be depleted will be higher. -
if you do run out of capacitor power, your modules will turn off. That is all. You can still warp (albeit for a small distance and if you are not being “disrupted”) and your capacitor will eventually charge back up.
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fitting a ship to be “capacitor stable” is difficult. Fitting a ship to be “capacitor stable” without making large tradeoffs in performance is extremely difficult.
Generally speaking, almost all ships built with performance in mind will not be “capacitor stable.” This applies doubly so for ships fitted for PvP.
Instead, people learn to micromanage their modules… learning when to use a repair module and when not to. When to use an Afterburner or MicroWarpdrive and when not to. They use tactics other than raw stats and numbers to mitigate damage and maximize their own (see: range tanking, kiting).
This eases the burden on the capacitor (see first point).
And when all else fails… install a Cap Booster Module and fit it with the biggest cap battery that will squeeze in it. 