The SD card spec requires SD clock to supply for at least 74 clock cycles. On the other hand, the eSDHC controller in MPC8541 supplies about 13 SD clock cycles (with 180 degrees phase shift) at power up. Will SD card have any reliability issue by this fewer clock cycles than what is required by spec?
No, SD card should not have the reliability issue. 74 clocks can be supplied by setting SYSCTL [INITA]. The 180 degree phase shift will not affect card or eSDHC IP block's operation. The phase shift is due to the synchronizer.