Most do nothing to the signal via the analog inputs.
OK, maybe true for mine and maybe not - I can't find reference one way or the other to this in my receiver's manual. Once I get the Sammy (which looks like January at this point), I can do some testing.
I cannot imagine that individual speaker level adjustments would require re-encoding. Ought this not to be just a levels bias to the speaker outputs?! If that is the case, then "doing nothing" when the 7.1 analog inputs are used would require the receiver to reset the levels bias to zero when these inputs are selected (which would seem kind dumb).
Now for time delay (aka speaker distance), I can see how maybe re-encoding might be needed, but I would also wonder how listening critical that would be if your seating and speakers are well set up and your room is not huge.
Frankly, A bigger concern would seem to be lip-synch issues. I am more concerned about that as my video goes thru a Crystallio II VP. In the case of movies, this will be mostly 1080p/24 passed but will need anamorphic stretch in many cases.