Hi,
The KDB that you mention is related to QSPI Flash connected directly to the HPS pin and not the FPGA configuration pin. There will be no issue on connecting the MT25Q to FPGA configuration pin directly. You may refer to https://www.intel.com/content/www/us/en/programmable/support/support-resources/knowledge-base/component/2018/how-do-i-enable-micron-s-mt25q-support-for-eol-of-epcq---256mb--.html for the byte addressing mode.
For the reset pin, I would recommend you to weak-pull it so that the flash does not enter reset mode.