Why PJ0 and PJ1 are not reporting as PCINT pins
Majenko was very close but seems to have missed the explanatory comment from the source code:

// (I've deliberately left out pin mapping to the Hardware USARTs - seems senseless to me)
// Pins: 10, 11, 12, 13,  50, 51, 52, 53,  62, 63, 64, 65, 66, 67, 68, 69

#define digitalPinToPCICR(p)    ( (((p) &gt;= 10) &amp;&amp; ((p) &lt;= 13)) || \   
                                  (((p) &gt;= 50) &amp;&amp; ((p) &lt;= 53)) || \
                                  (((p) &gt;= 62) &amp;&amp; ((p) &lt;= 69)) ? (&amp;PCICR) : ((uint8_t *)0) )


Which seems like it may apply to the fact that the USART3 pins PJ1 (14) and PJ0 (15) are missing.

As for why providing mappings to the hardware USART pins "seems senseless" a little playing with git blame will show that these lines were added to this file in commit f179794  in response to issue 490:


  The SoftwareSerial library defines macros that map Arduino pin numbers to the pin changes interrupts on the pins.  We should pull this up into the board-specific pin definition header file so that the SoftwareSerial library can work on any AVR for which those macros (and the pin-change interrupts) are defined.


Which is to say that David Mellis didn't write those lines for generic interrupt use as part of pins_arduino.h, but rather moved code originally written as part of the software serial library to this file to make things more portable (and, though perhaps incidentally, generally usable for other purposes).  It's not exactly clear who the original author speaking as "I" in the comment is - the Mega-specific code in question appears to come most immediately from Mikal Hart's extension of Ladyada's Uno-only interrupt soft serial code (which did not have it) but there's also a comment in that seemingly crediting Paul Stoffregen (Teensy boards) for at least some aspect of the macro...

It does kind of make sense that someone writing a software serial library could consider using it on hardware serial pins pointless.  But counterarguments could also be made - for one example, the 16u2 core either uses or has experimented with software serial at some baud rates, and for another a software serial implementation could be a plausible way of overcoming swapped RX &amp; TX wiring, or a way of implementing inverted signalling logic when using simplified level shifters or talking to something which expects to.

Given that in its current location the code is no longer necessarily only for software serial use, it seems plausible that a carefully written and fully validated patch to make it more general might be favorably received.