well bin files you typicallly have to change the file permissions to be able to execute it by typing
chmod +x filename.bin
and then run
then to install an rpm you will use
rpm -ivh filename.rpm
as of difference...i can't really answer that, cause the way i look at it, is as long as your getting what you want, i personally don't see what the filetype has to do with making anything better...
if you download something, which could be a tar.gz or a tar.bz2, or even an rpm, or just a regular file that you have to make executable....in the end you are going to have what you want regardless of filetype....