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Yes your right. ModusToolbox doesn't allow selection of P13_5 even though its the one thats loaded. Not sure why, but needs to be fixed. Please populate the resistor R62 and unpopulate R61 and use P12_1 for now.
Also, note that you need not assign any pin for card detect in the configurator. In the firmware you can use any GPIO custom pin for Card Detect. Add the SD Host driver Cy_SD_Host_IsCardConnected() function with the __WEAK type to your code. This function could read the value from any GPIO pin and return true when the card is connected.
Thanks for clarificaiton.