EEngr noted:
But allowing systems to be certified by an organization that says "We don't know how this works" bothers me.
The regulatory agencies - be they the American FAA, European EASA, Japanese JAA, or whomever - don't have the knowledge that the OEMs (Boeing, Airbus, etc.) have which is why they are dependent on the OEMs to assist them in the certification process. And the OEMs themselves depends on the system sub-contractors to assist them in the certification process. Boeing and Airbus are not experts in Li-Ion batteries, so both were assisted by the subs developing those batteries to develop the certification and testing process.
And this practice is not just in commercial aerospace. Many industries depend on the assistance of those being certified during the certification process.
Having an open-ended investigation into batteries, electrical panels, loose bolts, etc. might lead regulators to a root cause that Boeing won't like.
Why wouldn't Boeing like the identification of the root cause? Knowing how and why something happens is an important step in determining how to prevent it from happening again.