No, CONF_DONE and INIT_DONE signals should not assert high during Intel® Stratix® 10 JIC file programming.
When using Intel Quartus® Prime Pro programmer version 18.0 to configure an Intel Stratix 10 device with the helper image (Factory default SFL image) during the JIC file programming process, you may observe unexpected CONF_DONE and INIT_DONE signal assertion. The helper image (Factory default SFL image) only contains firmware data and not the full configuration data. Thus, the Intel Stratix 10 device has only been configured with the firmware data and even though the CONF_DONE and INIT_DONE signal are asserted high, the Intel Stratix 10 device has not yet entered user mode.
In Intel Quartus Prime Pro programmer version 17.1 and earlier, the CONF_DONE and INIT_DONE signal are expected to be asserted high as the helper image (Factory default SFL image) contained full configuration data.