In this context, it's the DOJ chain of command. This sort of memorandum isn't something that will impact a person's day in court directly should they be prosecuted; it indicates to prosecutors what the Executive branch would consider a "career-limiting move" to waste public resources prosecuting.
Compare with the Obama-era guidance about federal drug law enforcement in states that had decriminalized marijuana. Technically, marijuana never stopped being a (federal) controlled substance, and every state grow operation and distribution center is in violation of federal law. Obama made clear that enforcing that law in those states would be a great way to send a strong signal to one's boss "I'm comfortable at my current level of achievement and feel no need to ever be promoted in the future," and that policy basically hasn't changed in the intervening two administrations. But the federal law is unchanged on the matter.
Fully disagree. I can think of many situations where you talk your way out of charges. One is a traffic ticket. Another is a domestic dispute where someone is making false accusations about you that are easily disproven.
"good faith" is determined by how much money and power the internet service being audited has. If they're rich or powerful corporation or celebrity then it's in bad faith. If it's some mom and pop webstore then it's in good faith. The FBI are just hired goons for the powerful.
"If you have something illegal on you, tell me now, because I won't be able to help you later"
Police had no intention of "helping" anyone, this is a lie that makes life easier for police and prosecutors when it comes to charging an individual.
Would I be acting in good faith if I expect a monetary outcome for my research?