^^^ All this.
One of my first instincts was "don't trust the guitarist's opinion on where the bass should sit in the mix." And i say that as a bassist and a mix engineer.
All joking aside, there are way too many variables going on to make a universal assumption about one person's opinion about one song at one rehearsal using different basses. So don't take as gospel what this one guitarist thought worked better for the mix in the one situation in this one room with a lot of variable changes. It might be true this time but not next.
Yes and no.
Do they sound different? Yeah. But also, a J bass sounds different from itself depending on if you use the neck pup, bridge pup, or some combination of the two. And also every bass sounds a little different. Every P bass sounds a little different from every other P bass, and they all sound like P Bass.
These statements are a hint, perhaps?
It seems like you're making EQ adjustments with the bass in isolation for your own ear and not for each bass in the mix while everyone is playing. That plus the volume adjustment.
- Maybe the P bass fit better in the mix and was louder because its frequency response curve suits the sound and the guitarist's ears better.
- Maybe he could hear it better because it was just louder, because you turned up the volume.
- Maybe it was because your "arbitrary" EQ adjustments for the P worked better in the mix than your EQ adjustments for the J. (Arbitrary meaning "to suit your tastes" not "to suit the mix")
- Maybe it was just that combination of P plus Amp plus Room plus all the tones the other musicians in the band were using for that song.
All this was a long way of saying, don't sweat it too much. The two basses sound different, but not so different you couldn't make either work tonally for your band if you spent some time dialing both of them in, in the context of the mix. They're both great basses.