as for "Who makes up these rules?" - that's the great unknown. the reality is that there were mixed standards, just like for spelling, for decades. finally, some newspaper decided to not only clean it up for their own writing, but to actually publish what they chose to use since they get so many submissions from non-employees.

I believe the Chicago Tribune set the current style, if my memory recalls this conversation from some 16 years ago.

However, I just looked up "ACS Style", and what came up was Oxford U Press, which did the outside-the-quotes version. :)

Actually, here's an ACS summary:

4. Placement of punctuation with quoted material. ACS style differs from some standard English practices concerning the placement of punctuation around quotation marks.

a. When introducing a quotation that is a complete sentence, do not place a comma before the opening quotation mark and do place the period inside the closing quotation mark if the quote ends the sentence.

The Nobel Prize-winning physicist Isidor Rabi said “If you decide you don’t have to get As, you can learn a lot in college.”

b. If a punctuation mark is not part of the quoted material, do not place the punctuation within the closing quotation mark.
The manufacturing process the scientist invented was “new”.

I would note that in addition to that, the count of commas involved in a list is also subject to variation.

a, b and c

vs

a, b, and c

or the "oxford trailer":

a, b, and c,

I perfer the middle. leaving a comma out can presume that two items are associated, as in

a and (b and c)

which while mathematically is irrelevant, in english it can be deceptive in its connotation.