The SoC Hardware Library (HWLIB) configures and controls the SoC Quad Serial Peripheral Interface (QSPI) Controllers.
The QSPI HWLIB source can be found in the /ip/altera/hps/altera_hps/hwlib/src/hwmgr/alt_qspi.c file.
The alt_qspi.c file in the 15.0 and earlier releases of SoC EDS contains the definition of the function alt_qspi_device_read_config_set, but does not provides the functionality to wait extra clock idle time when necessary.
To workaround this problem, a simple counter can be added in the alt_qspi_device_read_config_set function declaration to add the possibility to wait for extra clock cycles when alt_qspi_is_idle() == false.
This problem is scheduled be fixed in a future version of the Altera SoC Embedded Design Suite.