My tools for color profiling are rather rudimentary by the standards of those who are hardcore into these kinda things.
For LR, I use the Spyder Color Checkr and their associated software to create profiles for different lighting conditions (For each camera, of course), tweak a bit to taste and save them. I use these as starting points.
For C1P, I shoot the Spyder color checkr in different lighting conditions, use a default color profile as starting point, use auto adjust, then do the fine tuning using the color editor and save as ICC profiles.
You"re definitely right that Photographers can benefit from doing custom profiling instead of sticking with the defaults. My cameras, across formats have benefited from this, but I maintain that the difference in color fidelity between MF and smaller formats still remain after this.
Regarding Adobe, it's not just the color rendering that I dislike about their RAW converter. Their default output requires quite some work to match the sharpening of C1P, lacks some features such as corner sharpening for WA lenses, lacks fine tuning tools such as the skin tone editor and so on.
In general, I only work with LR when I have a large batch of images to finish (Such as vacation pictures, which I am doing right now). Adobe certainly has a better library management module, but that is where my praise ends.
I missed the 200% thing, which as you say is of course not profile related. The D800 has aa filter which makes its blowup quality better due to less aliasing, but many photographers has developed a pixel peep taste that prefers aliasing artifacts over correct micro detail. And indeed remove the aa filter and have sharp lenses you get those "desirable " artifacts. Today 135 has that too though, so it's not format related. MFD has a lead though due to overall sharper lenses, especially in tech cams like I use myself.
Yes, the AA filter in the D800 does play a part in that, but I have observed the same with an AA filterless camera such as the D7100 that I owned for a while too (Granted, this is only APSC). I do not have access to a current AA less camera such as the A7RII to do side by tests, but you might be right, the difference might be lesser now.
Good point on the lenses as well. I do not have tech lenses, but the Schneider Kreuznach lenses for Phamiya are quite excellent IMO. 135 format has excellent lenses too, but the dud-to-excellent ratio is a lot more lopsided there.