Since you shared your bootloader architecture, I wanted to share a tool that my work finds useful that for working with the multiple binary files that are to be flashed to hardware.
SRecord (tool not the file format) for working inserting data into your binary files? For work we use a combination of SREC and bin files and each we embed similar data as to what you describe and the process was automated with Python before. Since we found SRecord, we replaced the custom Python programs with SRecord and now just use Python as a wrapper around SRecord.
SRecord has some nice features in that can be used to calculate and generate a CRC, extract ranges of memory, merge multiple files together, fill ranges with a a specific value and it also works with many different file formats.