For anyone encountering the same, the issue was that the asm/arch symbolic link wasn't being created to point to asm/arch-mx6. Adding the below the Kconfig in my board folder resolved this issue.
config SYS_SOC
default "mx6"
The error after fixing that is:
In file included from board/freescale/mx6ul_customboard_v1/mx6ul_customboard_v1.c:12:0:
./arch/arm/include/asm/arch/mx6-pins.h:47:2: error: #error "Please select cpu"
#error "Please select cpu"
^
scripts/Makefile.build:280: recipe for target 'board/freescale/mx6ul_customboard_v1/mx6ul_customboard_v1.o' failed
make[1]: *** [board/freescale/mx6ul_customboard_v1/mx6ul_customboard_v1.o] Error 1
Makefile:1257: recipe for target 'board/customboard/mx6ul_customboard_v1' failed
make: *** [board/freescale/mx6ul_customboard_v1] Error 2
Looks like for some reason CONFIG_MX6UL isn't being exported. Can anyone explain where this should be getting set?