Exactly, Tai. As I said, same design, but he was just a robot built by Wily.
And to build off of what Spectro said, the only reason Navis can battle is to protect their Operator's comps and their PETs from viruses. Naturally, Navis battling each other grew from that. Most Navis don't even have their own weapons like the GutsPunch or Rockbuster; some can't even fight at all (like Silk).
And unlike Yu-Gi-Oh where, as someone said, a person who murdered his friend will just duel you, some people in EXE-land will kill. See the fools at the end of EXE6 who, upon losing their Navis, decide to use their own bodies to attack Netto, since he's a puny child and doesn't have Rock's power at his disposal as in a NetBattle.