The way I typically look at this scenario is that Goten & Trunks didn't notice a difference between Super Boo and Innocent Boo. Their original estimates regarding Gotenks Base Post were heavily implied to be superior to Gotenks SSj Pre (Perhaps they were, for now we'll assume they were); while simultaneously believing themselves to be about equal to him in their Base form. So by their estimates:
Super Boo (Initial) =/= Innocent Boo (Full Power) =/= Gotenks Base Post > Gotenks SSj Pre
However, we're shown that they are completely wrong and both Gotenks Post and SSj Pre were actually significantly weaker then either Boo.