Actually, wc3 saves anything that is in the instance of a map... that includes custom systems and such... So the above reason is invalid...
If you want a reason on why we use Custom Save-load systems on ORPGs, I'll give you two: Compatibility and Portability
As I said, wc3 saves anything about the map instance, which includes the details about the map itself (filename, file path, map version etc)... now even a minor edit of the map which the save file uses, will invalidate the save file because the map data it has won't match with the new map data... I think even renaming the map invalidates the file... And as you know, most ORPGs are constantly updated so if we're gonna use the save system that wc3 has, no one can load their save file from 1 version of the map into the other since wc3 won't allow that... So if you want to play on another version of the map, you'll need to start from scratch again...
As for portability, the code output of custom Save-load systems is a lot more portable than the save output of wc3...
That's just two, but I think they're already more than enough to explain the reason why we use Custom save load systems...