www.makemkv.com

I find it strange that MakeMKV takes it upon itself to skip certain files in backups, e.g. PS3_DISC.SFB, zips at the root, etc. In the interest of preservation, it'd be nice if there were an option that forced MakeMKV to not skip anything.

For preservation you can use DiscImageCreator or Redumper like the ReDump project does: http://wiki.redump.org/index.php?title=Dumping_Guides

I don't think, it is upon MakeMKVs target to do such a thing.