I haven't used a parallel JB and an EJ Custom in the same position of the same guitar. However, my experience with both in separate guitars leads me to think of both of the EJ Customs as slightly "meatier" pickups than a JB in parallel in the bridge position.
Keep in mind that the EJ Customs use an interesting combination of specs that are not listed by DiMarzio: a lower number of coil windings and narrower gauge wire than your typical Gibson style humbucker. This results in different coil dimensions than a JB, even if you are close in inductance running the JB in parallel, and you have somewhat "normal" PAF-esque resistance. And coil dimensions do matter to some degree (at least according to Seymour Duncan, Bill Lawrence, and other pickup makers who've published their opinions on the matter). Look at an EJ Custom from the side, and you can see that the bobbins are only holding perhaps 70 percent of the amount of wire that they are physically capable of holding – making them electronically a narrower pickup (like, ahem, a Filtertron). And they use a brass baseplate, though there is still some debate about whether that makes a tonal difference vs. nickel silver. I say very little, personally...but maybe some small degree darker in tone.
At any rate, there is more than inductance to it. Construction details can make tonal changes as well. And let's not forget that just because two pickups are powered by A5 magnets does not mean that they both have the same strength. There's all sorts of variation in magnets from supplier to supplier, and even from batch to batch...then you've got pickup makers possibly tweaking the magnetic strength in house as well.
Bottom line, you can compare inductance figures and get some rough information...but it's just rough if there are other variables at play.
