Hi mate,I had a 2006 e46 m3 6sp man a few years ago...very nice cars with awesome build quality...the rear cracked boot floor is the rear subframe...lift the carpets up & check the boot floor for any cracks around the edge of the boot..
Also make sure it's done the running in service when new...also listen for any clunk noises from the rear that might lead to a faulty rear diff or might need a oil change
M3 cutters are a very good & friendly forum
Goodluck with yr search mate