Using your example # 1, Mr. Woodget, I would either make mine by base figure or by project.  If I just wanted creature versions of a figure with no immediate intention of using it with any other figure, I would have it in a sub folder of the figure's Runtime.

Example:  Runtime:  Victoria --> Victoria 4.2 --> Monsters --> Vampire (folder, as there will probably also be clothing or props that are classified as figures)

If I were starting a project where I would actually use the creature, I would start a new Runtime and immediately copy into it everything I thought I would need for that project so I can find it all in one place.  This helps me 3 ways:  I can just link the 1 Runtime and not have to scroll down (yes, we can number or put a ! to bring it to the top, but why bother?), it gives me an extra copy of whatever just in case something happens to the original and I either forgot to back it up normally or I misplace the backup, and all of end products are stored in the same place instead of "Victoria's Vampire Dress" only in Victoria's Runtime + "Mike's Bloody Corpse" only in Mike's Runtime + "Gothic Graveyard" only in Locations Runtime.

Otherwise it is Select Runtime + Select Library Tab + Select Folder + Select Sub, repeat for next Runtime, Render, Save Where Again?

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Your 2nd Question:  Since I do not use much or anything made with morphs from more than once source, I cannot really advise you on this.  Since you do not want to duplicate the files, * I * would just put all V4/A4/Whatever in my existing Runtime:  Additional Figures, since those characters can be used by more than one figure UNLESS they have to be in the same Runtime as the base figure, but I think you can tell Poser where to look, even in a different Runtime, and just have it cross reference automatically after that (unless you move something later, then you just have to do it again).

Your 3rd Question:  Answered, really, by my Per Figure If Specific / Additional Figure If Multi Use / Project system.

The only folders that get changed "regularly" are in the Project Runtime since I already copy everything I think I will use and treat the other Runtimes like source material.  Those rarely have anything altered, just new things added from time to time.

At the risk of sounding redundant (again?) and, as I am getting hungry, I will use soup as my example.  The bowl is the Project Runtime and each type of ingredient is brought over from somewhere else:  Water from the sink, veggies and meat from the fridge, seasonings from the pantry.  Getting everything ready and cooking it is what Poser is for.  If I did a good job, I enjoy the soup.  If not, I can make minor adjustments but, if it really sucks, I just start over or go hungry.  As long as I do not burn down the house, I should be fine. :)