You're right, it's probably not going to make much difference, but it might...and this of course depends upon how you will play/modify, etc., the files.
A clone is a 1:1, bit to bit copy; very little modification is available in this mode. You can elect to copy the .IFO files or not, . Pretty much everything else will be copied. No compression is possible in this mode
Full Disc will also copy the extras...special features, menus, etc., but will allow for some additional mod. For eg., you can compress in this mode, alter the title-playback order.
I'd experiment with each to see what best suits your needs. Just rip 'em to your hdd so as not to waste media
Also, take a look at the Fab tutorial & manual for more info.