It's obvious that having a choice of having both shutterspeed and aperture rings coupled or not (CF and later versions) is more convenient than having them coupled all the time. Is it not?
The thing that should always be high on the list when buying used stuff is age.
You never know what a bit of equipment has had to put up with since it left the factory. So look for how much chance it has had, how much opportunity there has been for it to have been abused. The younger, the better.
But it of course is not the begin all end all. Old stuff may still have lots of usefull years left in it. It also depends on how well built things are to begin with (in another thread we can read that there are no 'professional' cameras. Well, there are. Some are made to withstand continuous hard use. Others will start needing things repaired and replaced after a trifling 10 years of day-in day-out use.)
And as long as there are still people capable of giving proper attention to maintenance and repair of old stuff, age becomes even less important.
The optics of most lenses have not changed indeed.
There are a few notable exceptions. The 40 and 50 mm lenses mentioned are among them.
The FLE CF or CFi version of the 50 mm Distagon is indeed to be prefered over the 'regular' CF or C version.
But not that the non-FLE was a bad lens. It wasn't, isn't. It's just that the FLE is a better lens.
The 500 mm Tele-Apotessar, and the 350 mm Superachromat are also optics that were improved over time.
The 60 mm plus 120 mm set would be a good one. Very versatile.
I use a 60 mm plus 150 mm in my 'walkabout without a specific purpose'-set, and i can't remember when i last wished i had another lens in my bag. A 120 mm obviously is very close to the 150 mm, and would do just as well.
But you will eventually want to add lenses. A 40 mm at the wide end, a 250 mm at the long end, and something in between too (the 80 mm - much maligned - really is a great lens!).
Apart from age, the difference between a 500 C and a 500 C/M is that you can change the focussing screen in a C/M yourself. Of the two, i would pick the 500 C/M.
Both offer mirror prerelease (not "lock up" - mirror lock up is a thingy that (guess...

) locks the mirror in the up position, i.e. puts it there and keeps it there, no matter what else happens. Despite the widespread misuse of the term, very few cameras offer mirror lock up. Of the Hasselblads, only the 2000-series cameras do).
But i'm sure you meant prerelease (the mirror is moved up before the exposure, allowing any movements it causes to dampen before the exposure is made. It comes down again as soon as you rewind the camera), so: yes.