Well, if they ask the FIA, and the FIA tells RBR and Ferrari that they think what Mercedes is doing is legal, then it would be logical to assume they themselves have something they're working on. So in practice it amounts to clarification, besides its not like the FIA makes a habit of making sudden changes that affect Mercedes negatively, they have historically had time to develop counter measures. The delay of oil burning clampdowns, delay of banning DAS, although it's good to see the FIA being fair and giving RBR and the other teams time to strengthen their flexy wings as well. So even if by some form of happenstance, the FIA makes a change against Mercedes, I'm sure they'll have time to develop a countermeasure. They have an extra 1.2 million to spend now, so It'll be fine.
I doubt it's them knowing any inner workings of the Mercedes power unit, probably just got an idea wondering what they're doing. People are allowed to contemplate and form ideas and use their imagination, within reason of course.