I think it's more a question of the JB being matched to the right guitar. Too much lower mids, it gets flubby. If the guitar is naturally thin, the JB usually sounds annoying. In the right guitar, it's awesome.
Also true that amp, speakers, and EQ matter. Cut bass before hitting preamp, beef it up in the effects loop/power amp sends is very standard metal tone technique (done any number of ways, from cutting bass with dirt boxes to graphic to parametric EQs).
Mustaine is also a ridiculously tight rhythm player. Who isn't afraid to leave room for the bassist to work. A lot more comfortable with mids than most speed metal players. [Except on Countdown to Extinction, where he may have used a different pickup for some of the rhythm parts, and VHT power amps, which didn't last long before he went back to his Marshall dual 100W monoblocks.] Dann Huff got him to try other gear for Risk & Cryptic Writings, too, but he still wound up right back at the JB as his bridge pickup and Marshall dual 100W monoblock power amps into his same 4x12s again for his live rig.