I think you're right to a point. Lots of these basses we're talking about (the Stingray example above being chief among them) have their signature tone in part because of the pre. You choose a Stingray because it has that sound, if you find you need to make drastic EQ changes to make it sound good you've probably picked the wrong bass
There is no absolute "flat" from which to get all the tones you want with EQ. If a bass does it for your ears, for whatever reason, then rock it out. Track it, gig it, make it do what it do
Also flat into an interface is not really representative of electric bass tone (the amp is a massive part of the equation as somebody else pointed out). Even if I'm tracking direct it's typically with an outboard pre. For serious recordings its a couple mics on a cab or two and a DI.