Emulate non-standard keyboard from Arduino
Emulating a keyboard matrix is actually harder than you would at first think. It's not just a case of setting certain combinations of pins as HIGH or LOW - you need to actively monitor one side of the matrix as it sweeps across each row and control the other side depending on the buttons that are pressed or not pressed on the current row. And all that has to be done fast enough that the C64 doesn't see buttons constantly bouncing up and down.

Further, you really need all your outputs to be open drain so as not to interfere with each other or the rest of the system (depending on just how the C64 system works), and Arduinos can't do open drain natively - instead you have to emulate it by switching between INPUT and OUTPUT + LOW which adds extra latency.

If you only want access to a few of the buttons a better arrangement would be to add a small N-channel (logic level) MOSFET or an NPN BJT between the two sides of the matrix for whichever button(s) you want to control (check the schematics for which pins and which way round to connect it). Activating the transistor would then be the same as pushing the button down. It can even be in parallel to the existing button so as to not break the keyboard.