Sorry for the delayed reply. Since the forum migration, I apparently stopped receiving notifications for some Automation Blocks questions, so I’m only catching up on them now.
Paul’s suggestions are the best practical solutions here: for transitions, Sequence > Simplify Sequence with Remove Transitions enabled is a good way to create a clean copy of the sequence without the unwanted transitions. For effects, Edit > Remove Attributes is usually the right built-in Premiere command to try.
Regarding Automation Blocks specifically: currently there is no dedicated block for removing applied effects or transitions from clips. Some effect parameters can be modified via scripting/custom code, but removing applied effects is not exposed cleanly enough in Premiere’s classic scripting API to make this a reliable Automation Blocks workflow.
So for now I’d recommend using Premiere’s built-in cleanup commands for this. I’ll keep it in mind as a feature request, though, because bulk cleanup tools like this would definitely be useful.