You have made the assumption that the hex file is a 1-to-1 representation of the bytes in the flash. But if you look at the hex file (you can open it in a text editor), you'll notice that it is a text file.

It has a density below 0.5, i.e. there are on average more than two characters for every byte in the flash. The exception is if the addresses specified in the hex file creates caps - then a tiny hex file can span a huge address range with few lines of text.

Most compilers (actually linkers) gives a message last in the build step, giving a summary of consumed flash + RAM. Best information is available if you turn on generation of a map file, and takes a closer peek at this file.