In order to create Quantum Entangled Singularities (https://ae-mod.info/Quantum-Entangled-Singularity/) you need to use an explosion on a Singularity + Ender Dust, however, with explosion item protection on it becomes impossible to create one. Would it be possible to add a special rule to allow these explosion based crafting operations to work?

I don't think there is any generic way to recognize crafting recipe use cases. I think the best option would be to just add a blacklist for entities or even specific items contained in vanilla EntityItems to exclude from the explosion protection. It looks like AE2 has their own entity for the singularity, meaning that the entity blacklist should work.

I uploaded version 1.5.0, which blacklists the AE2 Singularities by default. It seemed to work in my testing, but let me know if there are some issues.

Thank you, looks like it works perfectly out of the box.