Yes, that patch is not a great solution. Ideally there would be an interactive choice in the gpg CLI between encrypting/signing subkey during the add-existing-subkey operation.

For anyone stumbling across this issue I created a docker image containing gpg with the patch above applied: https://github.com/smlx/gnupg-piv-agent

Note that I'm referring to file based keys, not card based.

I tested this on 2.3, and it doesn't seem to be fixed. When adding an existing ECDSA subkey I don't get the option to choose whether to make it a signing or encrypting subkey. Instead it only allows me to choose an encrypting subkey.