Need help with programming PYNQ-Z2 via JTAG while boot jumper is in SD card mode

Yes, you can ssh and develop there. Or also open a terminal in JupyterLab and lunch a terminal.

You can also check this post:

For the ILA, you need the JTAG.
There was a contribution from the community not to use JTAG, you can check it here:

https://pynq.readthedocs.io/en/latest/pynq_libraries/debugbridge.html

Mario