I've worked on all 3 production years of Blaster 1's, I haven't seen them come with a cluster before. There is a chance though that somebody just decided to replace a crusty e-box with one from a Raider or Wave Venture. Both of those have a 3 connector harness, and if you know for sure your e-box is original then most likely Yamaha just decided to start using a three connector harness as the universal harness for all following production years with similar electrical schematics.
62E-82553-00-00 Wave Blaster 700 - 2 connectors
62T-82553-01-00 Wave Raider 700 - 3 connectors
63N-82553-00-00 Wave Venture 700 - 3 connectors