Hi,
your "IDN first command" is not an IDN command. This is various frames sent after the startup sequence:
01="Reset" followed by 03 03="SPI poll" followed by 00 55="SPI send command Echo" and there is an unexpected 00 being printed in front of this line (please check your log and make sure to follow the SPI CS signal to split the MOSI data into frames).
For your reference, I've downloaded the binary provided inside the X-CUBE-NFC3 package on my board and here is the commented output from the logic analyzer:

Feel free to connect a logic analyzer on the SPI (CLK/MOSI/MISO/CS)+IRQ_OUT+IRQ_IN and to send me your trace. Also, make sure your logging is correct (the very first 00 is either a logging issue or an expected character being sent due to one of your changes in the original code).
Note: The ST25R95 datasheet contains the description of all the commands being used in the X-CUBE-NFC3 firmware.
Rgds
BT