Concern is not about data width, but about pins corresponding to data bits 2 and 3 when QSPI is configured for 1 bit mode. According to RM Rev. 5 pages 1192-1193 these pins are always driven by Vybrid, and pin levels are set up using ISDnFx bits in QaudSPIx_MCR register. But RM doesn't tell which bits in QaudSPIx_MCR are actually ISDnFx bits. I have MQX installed on my PC and found and see there MVF50GS10MK50.h file. Unfortunately it also doesn't list any ISDnFx bits. Only following MCR bits are defined.
#define QuadSPI_MCR_SWRSTSD_MASK 0x1u
#define QuadSPI_MCR_SWRSTSD_SHIFT 0
#define QuadSPI_MCR_SWRSTHD_MASK 0x2u
#define QuadSPI_MCR_SWRSTHD_SHIFT 1
#define QuadSPI_MCR_DQS_EN_MASK 0x40u
#define QuadSPI_MCR_DQS_EN_SHIFT 6
#define QuadSPI_MCR_DDR_EN_MASK 0x80u
#define QuadSPI_MCR_DDR_EN_SHIFT 7
#define QuadSPI_MCR_CLR_RXF_MASK 0x400u
#define QuadSPI_MCR_CLR_RXF_SHIFT 10
#define QuadSPI_MCR_CLR_TXF_MASK 0x800u
#define QuadSPI_MCR_CLR_TXF_SHIFT 11
#define QuadSPI_MCR_MDIS_MASK 0x4000u
#define QuadSPI_MCR_MDIS_SHIFT 14
#define QuadSPI_MCR_DOZE_MASK 0x8000u
#define QuadSPI_MCR_DOZE_SHIFT 15
I guess that perphaps Vybrid doesn't drive QSPI bits 2 and 3 in single bit mode. Unfortunately I don't have working Vybrid board at hand, I'd like to check if these pins are driven in single bit mode.