Since the main thing you want to avoid is using the same card for Prosperity-deciding and Dark-Ages-deciding, Option 3 seems closer to the intent than Option 2.
No, the thing you want to do is have the chance of using Colonies be proportional to the number of Prosperity supply cards and the chance of using Shelters be proportional to the number of Dark Ages supply cards. Option 2 is correct (and different from Options 1 & 3 which are, as reported, the same)
I trust the user who's name is a math pun.
The last part of the discussion revolves around the interpretation of
... Do not use the same card to choose ...
Some people interpret this as
... Do not use the same card draw to choose ...
These people are content if the second draw happens to be the same card as the first draw.
Others require the second card to be different.
I also think this is wise. I think that the rules could be interpreted in different ways, which are all fine in practice (hey, do what makes you happy, right?).
In my interpretation, both Prosperity and DA rules have the following:
the use of [Plat+Col / Shelters] should be determined randomly, based on the proportion of [Prosperity / Dark Ages] cards in use.
As a math person, this clearly says that if X out of 10 of the kingdom cards are [Prosperity / DA], then there should be a 10X% chance of using [Plat+Col / Shelters]. Option 2 satisfies this, but not options 1 and 3. At the same time, the suggestion of not using the same card to decide Plat+Col and Shelters can be interpreted to contradict this. Here, I agree with the excellent point of jeb56, that it can also be interpreted to mean that you use a different card draw to determine Shelters.
Anyway, as I said, both interpretations lead to fine results, and people should do what seems right to them.