It seems only one instance of QPSI is supported but 3 instances for SPI.
However for those single byte commands, they are transmitted as standard SPI signals regardless of SPI.transfer or runCommand.
0x05 seems to be querying if the flash is busy or not and should not cause adverse effects.
Congratulations to your latest achievement in the current consumption. Although there are still unknown questions, your example provides a workaround to drive nRF52840 to its extreme performance, well done !!