Shinji's strategy was for Bossgodora and Toritodon to be defeated to make Satoshi think that he was gaining momentum. In the Japanese original, Shinji says Bossgodora and Toritodon were willing to carry the role of being defeated.
In the English dub, Paul states that he purposely let Ash take out Aggron and Gastrodon but doesn't say anything about them being willing to play that role in the battle.
Paul: I purposely let you take out Aggron and Gastrodon so I could be certain of your strategy and exactly which Pokémon you'd use.
Shinji: For that purpose, those two were willing to carry the role of being defeated.
（シンジ）: そのために あの２体は倒れる役目を進んで担ってくれた。