A.)  I never just install a DL.  I always extract to a seperate folder; rename the each directory(Except Geometries, Props, and Textures) to the same thing.

B.)  A typical Scene for me involves alot of work on just one figure.  I find no problem locating things organizing Character, then by Technicality(MATs, MORs, Clothing, Favorite Character Sets.)  Then by Figure Parts(Especially for MATs, i.e. Head, Body, Eyes, etc.)  Even if I spend a time/day(s) going through my M3 stuff for V3.

C.) Not having seperate Runtimes requires a certain behavior.  If this is your computer, you'd like to use Poser alot, and do'nt mind using Windows, Hibernation, then one Runtime would work great.   But if you think you'll be opening and closing Poser frequently, it will add a minutes to your load time.