As a die hard Scooby fan, it should be listed twice IMO. The way Scooby shows are packaged and syndicated after the second season of Where Are You gets pretty weird until 13 Ghosts which makes it annoying as a fan to chase down and buy every episode, etc for anything that aired between.

The third season of WAY was planned and first aired as part of WAY for the first eight episodes including having the WAY opening and closing credits. The final episodes first aired under The Scooby-Doo Show as part of the Scooby's All-Stars block alongside Laff-A-Lympics and Captain Caveman and the Teen Angels. The first episodes were later re-broadcast as part of The Scooby-Doo Show including having the opening and end credits change from WAY to TSDS.

So S3 is this kind of weird state where half of it was first ran under WAY, the remainder under TSDS, and only later was everything re-broadcast under TSDS. This funky state is further reflected in the various editions of "Scooby-Doo, Where Are You!: The Complete Series" Blu-ray collections since 2019. All 16 episodes of S3 are part of the WAY collection, but they used the re-broadcast version that has the TSDS opening and closing credits.