Generally I assume you know what system default paths are for...
1)
STANDARD is anything not assigned to a bios/devices/software list. So it's a path for anything not special.
DEVICE is the system default path for devices (e.g. MAME got devices 22vp931, bsmt2000, mie, namco50, etc). There also exists MECHANICAL, if the loaded data contains MECHANICAL flagged items.
2) because MESS handles the rest as standard I guess and only these are flagged as BIOS
3) most likely because they are empty. If cmpro imports software list via exe import it runs the exe with -listsofware name_of_the_list. If that ends up with no result, the list isn't listed.
4) Sysdefpaths have to be unique per software list. BIOS/STANDARD/DEVICES/MECHANICAL can share the same but software lists can't share the same path. Well, there is an auto-assign button which maps your setup rompaths to the sysdefpaths but it will look for exisiting files in these paths and the best match will win. If you paths are empty (which I assume if you start) that option won't help you. So if you don't have any files for the several lists, you need to go through the assignment hell once.
Of course this only applies to the multi-software list support within one profile. Noone stops you to simply load the software lists xmls separately in the profile (or via the batcher)...then you don't need to fight with sysdefpaths at all....