Hi Max,
SEC tool does not use JTAG, SEC tools talks directly with the Serial Downloader implemented in the device ROM. I do not know what HW you use - your proprietary or still NXP EVK?
If proprietary then you need to look to the Reference Manual (if link works, it should be accessible from here https://www.nxp.com/products/processors-and-microcontrollers/arm-microcontrollers/i-mx-rt-crossover-...)
then look to the chapter 9 System Boot - in short the device must start ISP - using either GPIO pins or fuses and then communicate with ROM via USB1 or LPUART1, see here

More details can be found in the mentioned RM. IMHO the problem less should be the serial communication with proper USB to serial converter with proper voltage levels.
Regards,
Libor