Concerning the distance info, your explanation sounds right. I was not aware of that, nor do understand why (given TTL exposure) the meter should be fooled into underexposing.
The Df was set to neutral with sharpening maximised (+9) as usual, to ease focussing in LV and sharpness check when reviewing the shots but, as far as I know, this does not affect the RAW files - only the in-camera jpeg. I always shoot RAW, and this is also the case here.
I only desaturated the greens (and the yellows to some extent) in the building shots to "neutralize" the green cast caused by the pond. In the first shot, I reduced the blue luminance, to somewhat obscure the sky reflections and increase the contrast.