I have solved the problem but i am not sure if its the proper way.
STEP0.0)
Burn the fuses via NXP-MCUBootUtility.exe.

STEP 0.1)
You need to modify in some project the const flexspi_nor_config_t qspiflash_config data structure present in "evkmimxrt1170_flexspi_nor_config.c" according to your memory. in particular change the .sflashA1Size field to .sflashB1Size.
I have made a blinky project for this test purpose.
Compile and generate HEX file with the new 512byte of memory configuration data that will be written at address 0x60000400.
Set your custom board to serial downloader mode and via NXP-MCUBootUtility.exe and connect to flashloader.

STEP 0.2)
In "Boot Device Memory" page, browse your HEX file and put the data into qspi memory present at FLEXSPI2 instance B port.
from this point if you put your bord into "boot from fuses mode", and reset it, it should start blink.

BACK TO FLASHLOADER USED FOR DEBUG WITH MCU IDE
You need to build it, there's no way to use existing ones. You MUST to do point 0.0 and 0.1 because the ROM API needs to find those 512 bytes at adress 0x60000400 or debugger will give the following error:
"Flash variant 'iMXRT1170_SFDP_FlexSPI2_A_QSPI Aug 3 2023 11:35:30' detected (0B = at 0x60000000)
driver describes no sectors starting at 0x60000000
Flash Driver V.2 startup failed"
Unzip the iMXRT117x_FlexSPI_SFDP.zip and open in workspace the project iMXRT117x_FlexSPI_SFDP and the LPCXFlashDriverLib.
You fill find them in C:\nxp\MCUXpressoIDE_11.6.1_8255\ide\Examples\Flashdrivers\NXP\iMXRT.
Use an existing build configuration (for example the MIMXRT1170_FlexSPI2_A_SFDP_QSPI) and build it.
if you get some errors fix the linker settings as follow:

Steps to modify the FLASHLOADER:
1) in test_main.c uncomment the line 63 "uint32_t FlashSize = flashConfig.memConfig.sflashB1Size;" and cooment the line 62 "uint32_t FlashSize = flashConfig.memConfig.sflashA1Size;"
2) FLEXSPI_NOR_INSTANCE must be 2 and FLASH_BASE_ADDR must be 0x60000000
3) Change the #define CONFIG_OPTION0 and #define CONFIG_OPTION1 to #define CONFIG_OPTION0 0xC1000000 and #define CONFIG_OPTION1 0x20000000. Those fields may change according to your memory - look at page 366 of processor reference manual
4) In FlashPrg.c lines 217-221 you need to modify the
FlashDevice.szDev = flashConfig.memConfig.sflashA1Size;
to
FlashDevice.szDev = flashConfig.memConfig.sflashB1Size;
Important: Dont try to define PORT_B or somehow the flashloader will crash telling you that it does not recognise the version.

5) Compile the flashloader.
6) Put your .axf file to your project folder and rename it to "somethingyouwant".cfx (the flashloader is recognized only as .cfx file).
7) In your project set the flash to 0x60000000 Location (That's FLEXSPI2 address) and change the flashloader to what you have created before.
Debug the project. In my case there's an error that i need still to investigate but click ok and go over.

Now you have the control of the debug procedure with standard breakpoint at main.

I hope that this helps you to get out of the imxrt flashloaders and spi alternative boot hell.