Does it have a “pass thru” mode so I can replace my PC keyboard?
Short answer: No.
Longer answer: I should be possible to use an adapter or so for using the keyboard of the MEGA65 for your PC. But as much as I know, it's intern not an standard USB keyboard. It has it's own programmable controller.
And at last an insider joke: MEGA65 has no USB connector, where you could connect your PC. 
If playing dead seriously now: Well, if someone is very serious it's possible I guess ... Some can write a simple MEGA65 program to output keypresses on the serial port of MEGA65, then there is a need for a Windows/Mac/Linux/etc driver which listens for the USB-serial at the PC/Mac end and tell the OS that it's a keypress ;-P So a keyboard driver for your OS on your PC. Or, someone is "crazy" enough to write a core for MEGA65 platform which implements a HID class USB device through some pins of MEGA65 (even on cartridge port, or whatever - a custom cable would be needed ...). But surely, this project is close to "insane" level in this form, not even counting the fact, that it would be a "bit" expensive keyboard if someone wants a MEGA65 just for a keyboard for the PC 
Indeed, MEGA65's keyboard is really nice, uses cherry MX switches AFAIK, so for a more practical solution, if someone needs a similar "press-feeling" keyboard, can buy a mechanical PC keyboard using the same cherry MX switches what MEGA65 uses (I'm not sure which MX though ...)
@LGB-N
Exactly what I though.
A Cherry G80-3000 keyboard with MX-keys costs about 100€.
You can choose silent or with click!
Cheaper and much more convenient than an adapter to connect the Mega65 for keyboard replacement to a PC.
You could certainly change the MEGA65 keyboard CPLD to support USB and than you could connect it to a PC, but the problem is, that certain keys would be missing and the kezcaps labeling would be useless as well.
The MEGA65 keyboard is designed to be an almost perfect Commodore keyboard, not a PC keyboard.
tbh, what i would be interested in, is once the MEGA65 keyboard is sepeartly available to change the configuration to use it with a Nexys4 fpga board. This would be a blast
If playing dead seriously now: Well, if someone is very serious it's possible I guess ... Some can write a simple MEGA65 program to output keypresses on the serial port of MEGA65, then there is a need for a Windows/Mac/Linux/etc driver which listens for the USB-serial at the PC/Mac end and tell the OS that it's a keypress ;-P So a keyboard driver for your OS on your PC. Or, someone is "crazy" enough to write a core for MEGA65 platform which implements a HID class USB device through some pins of MEGA65 (even on cartridge port, or whatever - a custom cable would be needed ...). But surely, this project is close to "insane" level in this form, not even counting the fact, that it would be a "bit" expensive keyboard if someone wants a MEGA65 just for a keyboard for the PC
Indeed, MEGA65's keyboard is really nice, uses cherry MX switches AFAIK, so for a more practical solution, if someone needs a similar "press-feeling" keyboard, can buy a mechanical PC keyboard using the same cherry MX switches what MEGA65 uses (I'm not sure which MX though ...)
No Panik, i wouldn't create a RemoteKeyboard
But you metioned a serial port. And i like serial ports. but till now i didn't find one on the mega65.
Is it one of the black sockets inside? Are they usable form the OS?
