both commands should still work, but the old one ( extjoe ) just set's the cvar ( jb_prefixaggression ) to another value.
so better use the cvar's, as far as they are documentated. but the functionality remains the same, i.e. everything can still be archieved by the commands listed in the readme.
once upon a time, there was only this extjoe stuff. then the bot was ported to metamod, and all those stuff remained, but cruft added this cvar stuff, that's this jb_* thingy. the extjoe stuff now only changes the cvars, i.e. the jb_* variables. we should have removed the old commands or left out the new cvars. so if you wanna change it, better remove one of the two.