Stack knobs give you a lot of tonal versatility, and even offer some sounds that you can't quite get with other control setups. Out of the 3 (Volume/3 way switch/Tone, Volume/Volume/Tone, and Volume/Tone stack knob), this configuration may offer the best benefit to a system where you have two different pickup types. In many situations, the P pickup can tend to crowd out the J pickup a bit in the sonic landscape. Many P pickups just have more output than a traditional(assuming you're using a single coil) J bass pickup. A lot of times with J pickups, you just want to find a balance between the two pickups that gives the tone you want, but a PJ setup is more of a balancing act.
Be mindful though that adding a second tone control and capictory will load down the signal a little. I had a bass where this totally fixed a pickup that was a little too aggressive, but with different pickups in that bass, it was too mellow. This type of tone control system may work very well depending on your needs though. The other downside, is that you have to twist more knobs to dial in a sound vs. some of the other options listed. This may not be an issue though. I found myself just dialing in the tone setting, and then adjusting volume to my needs on each pickup.
Not sure if that's a great answer, but hopefully it gives you a few things to think about!