In case there are no critical EMC or high speed signal issues, then normally the software engineer is allowed to dictate which pins to use and group them as per how the GPIO peripheral port registers are defined in the MCU. That is, your option "Connect them to pins that share the same register inside the PIC"
If you for example have some 8 bit "port x" register and mean to use 8 pins for a related purposes in software - lets say parallel input from an external 8 bit dip-switch or shift register - then you would use the pins corresponding to "port x", no matter where they happen to be located on the package.
The MCU manufacturer has already made internal EMC considerations regarding analog, digital and clock parts, usually keeping the oscillator pins or timer/PWM pins away from the analog pins etc.
Now in case you have sensitive signals like some high speed bus, high resolution analog signals, bit-banging to/from a RFIC or similar, then the PCB designer should be the one deciding which pins to use and the software designer has to adapt accordingly. Such signals should be given top priority in the PCB layout overall, which normally means keeping the traces as straight and short as possible, avoiding vias if possible etc.