I think on bodies and necks, there really isn't a whole lot of difference. Most of the time, I buy on tone and aesthetics alone. On fret/fingerboards, there is some tonal variation that I've noticed.
Personally, I tend to prefer rosewood and ebony fretboards, but that's all aesthetic based as I said. I tend to buy darker instruments. A yellow fretboard with a black or red body, or even a natural body, just looks weird to me. If I were to buy, say, a baby blue or yellow bass, then that may prompt me to consider a maple fretboard. Again, all aesthetics.
Realistically, I don't care what wood is being used for a body, though I do tend to end up with fairly heavy mahogany bodies, despite having a million issues with my spine. Why I seem to end up playing heavy instruments (hey, I'm saving for a Conklin GT7, which is far from light), is beyond me.
At any rate though, I just know what I like and I know what I can afford. A $5000+ custom instrument is just out of the question. Even if I were within the ranks of Geezer Butler, Alex Webster, or Geddy Lee, and had all the money I needed for whatever instrumetnt I chose to play, I'd choose to play instruments that are sub- $2000, especially if I were offered a signature model based off of what I was playing. The truth is that all these professional musicians attract new generations of players, and when a signature model is introduced, those starry-eyed kids want to go out and spend their hard-earned money of what their idols play. I had to work for every bit of bass gear I ever played on, starting when I was 16. Though I never was all that interested in a signature model, and still not, I look at all these instruments costing thousands of dollars and feel bad for those kids who want one, but it's completely out of reach. Hell...they're out of reach for some adults!
But back on topic, yeah. IF there's a difference, it's negligible and so slight that it doesn't even really matter. I don't buy basswood bodied instruments on principle, but that's me.