What is the rule that describes the use of "or" in these sentences?
"Do you want strawberry or grape jelly?"
"Can I drive the red, blue, or green car?"
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EDIT: I've misread the question. The OP wants to know about the rule (or possibly the role?) of "or" in the example sentences. I'll leave this answer anyway.
I don't think there is any rule, written or unwritten which I can refer you to.
But from knowing a little something about binomials when two or more words are listed, normally the polysyllabic word is cited first; e.g.
She doesn't like blackberry or apple juice
If one of the words is perceived to be more dominant, than that is nominated first; e.g.
It's a matter of life or death
Black or white coffee?
If one of the nouns is singular that will take precedence over the uncountable noun; e.g.
Do you want a sandwich or chips?
But if three or more nouns (or adjectives) have each a single syllable, share a common feature, and neither is considered dominant over the other, I'd say the shorter word goes first.
Which colour do you prefer; red, blue or green?
However, when it comes to the colour of flags if the colours are not separated into bands then it appears that red will dominate all other colours, if the flag does not have red, blue will dominate, followed by green and then yellow. The order will remain the same if the conjunction and is replaced by or but logically it would no longer refer to the colour of flags. Here then are just a few examples:
Wikipedia List of flags by color combination
For more help about the order of adjectives (excluding the order of colours) see the following question