While this still seems like an awkward solution, I was able to make a simple 'one-click' programmer for the RT1010 using a batch file and JLink script file.
The JLink script first loads and runs the nor_polling_transfer project, then loads the application image:
connect
halt
loadfile evkmimxrt1010_flexspi_nor_polling_transfer.hex
setpc 0x200001d0
go
sleep 250
reset
loadfile application_program.hex
reset
go
exit
I run this script in the JLink Commander with a batch file:
@echo off
JLink.exe -device MIMXRT1011XXX4A -if SWD -speed 4000 -autoconnect 1 -commandfile rt1010_program.jlink
I still think there must be a more elegant way to accomplish the initial flash configuration, but at least this method works.