Re: pickups with seperate outs.
No I don't have separate pick-up outputs, but I do customise my 6-strings a bit with switched pots, split humbuckers etc. On stage, these switches rarely get used, and I stick to the standard configurations.
I would say if it's between you and your laptop, by all means go for it as an experiment. However, the need for this is rather limited even for a six string where it probably makes more sense, and maybe some stage-stereo effects could be achieved. I think some Gibson ES-335 derivatives did this (ES-345, I think. The "S" is not stereo in this case, but "Spanish", that's a different story). For a bass I would think the mod would be even more limiting unless you're going for some real exotic tonal variations, very melodic bass patterns, slap-bass, etc. If I were you, when you have your soldering iron out, I'd go for a straight pot replacement for that errant tone control. It'll only be a few dollars. But if you want to experiment with separate outputs, go the extra dollar for a stereo jack and replace your current mono jack. All of this is only a few minute's job and completely reversible.
Still, I'd be interested in what you do, and what effects you get.
PC - i5 6500 3.2GHz; 16GB; Win10 on SSD + 3 other HDDs; 2 monitors in landscape; Sonar Platinum; Komplete 11, Steinberg UR22.
Instruments: Various electric and acoustic guitars, bouzouki (Irish), tenor banjo, 5 string banjo, lap steel, mandolin, bass, keyboards, fiddle. Marshall amps.
Listen to ... Cosmic Two-Step (2017)