I think I understand now...
For a long time... seadoo had a second flush port on the inside edge of the deck lid. Somewhere around 2007 (depending on the model) I guess they decided to save the $$$. The rear port has been on the pump flange since 98. (or there about)
Also... since the Rotax seadoo boats aren't rated to be left in the water... it's a moot point. Once it's on the trailer... just hook a hose to the pump port.
If you want an inside port... it's really not that big of a deal. Buy a Perko fitting, a plastic "T"... and a few feet of rubber hose, and add it. BUT... DO NOT plug off the rear port. That's an exit for normal water flow.