No offence meant. We can all see that you're the guy holding project together, and we all appreciate it greatly. As I read it, the bugtracker page you link to says that for security reasons the sys_boot5 pin will be linked to the Hall switch (which senses the state of the battery cover - i.e. battery cover off; sys_boot5=1), and that for additional security it may be possible to hardwire the sys_boot5 low, and hence override the Hall switch and not allow the boot sequence to be modified at all. Is this right?
sys_boot5=0: sys_boot[4:0]=0b10000 --> OneNAND USB UART3 MMC1 sys_boot5=1: sys_boot[4:0]=0b10000 --> USB UART3 MMC1 OneNAND