According to the UM10912, Chapter 5: LPC546xx ISP and IAP, Table 77.
IAP Read Boot code version number
Command: Read boot code version number
Input: Command code: 55 (decimal)
Result: Result0: Two 32-bit words. Word 0 is the major version, word 1 is the minor version.
However when executing this command the result is NOT two 32-bit words but two 8-bit bytes packed int Result0.
After executing the command the result in Result0 is 0x00001301 which means Major version 0x13 and Minor version 0x01.
The lower 2 bytes with major/minor version number is the correct output format.
The user manual is wrong, as a consequence this could also be wrong in some tools like the SDK.