I had a few Ideas for progmem, which won't work if the compiler removed unreferenced progmem data. So I did a bit of reading and it appears this isn't a bug and is actually set by the command line options.
-ffunction-sections and -fdata-sections, tell the compiler to place all function metadata in one location of the object file and, data into another.
PROGMEM on a variable tells the compiler to put the data into a completely separate section appropriately named progmem.
Next the linker receives a flag --gc-sections which allows dead code removal, but only from the function and data sections. All other sections will be linked 'as is'.