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lmao. Its due to so many pros upgrading their stock pups with dimarzio, seymour duncan and emg that these companies became famous in the first place. Same for baddass bridges. Pros upgrade their stock basses on regular basis
While other don't do anything like Les Claypool, John Patitucci and John Myung.
I know that John Myung, contrary to what was stated further up, has modded a couple of his basses. The Spector NS-2 that he used to record I&W was stock, and the Tobias Basic 6 that he used for a bit afterwards was also stock, as was the Tung that he used after that (though there weren't many Tung basses made so one could almost call them "custom built"). But, while his first Yamaha signature bass was always stock, the second one he had (RBX JM-2) had a second pickup installed with accommodating electronics about a year or two after he first started using them. To the best of my knowledge though he continued to use a stock JM-2 alongside the modded one for quite awhile.
In addition to that, he's had a modified Musicman Stingray for quite some time (since the I&W days even IIRC), the mod being a second pickup installed in the neck position. He's used that bass on one or two albums I think. Recently he has been playing stock Bongo 6 strings, usually HS but occasionally HH models. They're not modded but even more recently he's been experimenting with different dimensions and "body masses", so maybe that could count as modded? Not modded hardware, but modding the bass itself.
EDIT: A good point that was made further up, pretty much any artist that has a signature instrument is playing a modified instrument. You could call those signature basses "stock", but ultimately most of those players don't play those exact models that the companies sell, they play further modified and custom-made versions (despite the marketing)