We interpret your example as meaning there is one ball that has three colors on it. To distinguish two balls, we would write the sentence as “I found a blue ball and a red and green ball.” If we wanted to convey the discovery of three balls, we would write it as “I found a blue ball, a red ball, and a green ball.” If written as “I found blue, red, and green balls,” the sentence would identify three differently colored balls of an undetermined total quantity.

You may find our posts Lack of Commas Costs Company Millions in Dispute and Oxford Comma Dispute Settled interesting.
The natural pause you refer to is the joining of two independent clauses with a conjunction and a separating comma before it. We discuss this topic in our post Commas with Independent Clauses.

“I like apples, oranges and pears.” In this example it is plain that an “Oxford comma” would do nothing to add any meaning or clarity, as the meaning is perfectly clear without it.

“I like apples and oranges, and pears are also nice.” In this example the last comma is not the “Oxford” variety, and is required to indicate that what is about to follow the “and” will not be part of the preceding series. This comma reflects the natural pause in speech between the two clauses.

We agree that the Oxford comma or its omission should serve to clarify rather than operate as a fixed grammatical principle. If what appears to be proper punctuation instead adds ambiguity, the sentence should and often can be rewritten.

Consider the two example sentences in the article:
1. We invited our grouchy neighbors, Jan and Ted.
2. We invited our grouchy neighbors, Jan, and Ted.

The second sentence is clear. The presence of the Oxford comma signals two things – that the writer uses the Oxford comma, and that Jan and Ted have been invited as well as the grouchy neighbors.

However, the article states that “Including an Oxford comma can change or clarify the meaning. The first sentence identifies both Jan and Ted as the grouchy neighbors…”. However, in common usage, since the Oxford comma has not been universally adopted, its *absence* in the first sentence means nothing. Unless the writer has otherwise signaled that she is an Oxford comma devotee, the reader does not know whether the grouchy neighbors *are* Jan and Ted (Oxford comma convention) or could be (or not) (if the writer does not use Oxford commas).

As if that wasn’t bad enough, we can conceive of other situations when even the Oxford comma does not eliminate uncertainly. In sentence 1, the clarifying power of the Oxford comma actually comes only partly from the convention itself, but mainly from the fact that “Jan” is singular, so she cannot be the neighbor*s*. However, consider this sentence:
3. We invited our grouchy neighbors, the Jansons, and Ted.

Even with the Oxford comma, there is no clarity about whether the Jansons are the neighbors, or whether they are being invited together with the neighbors.

The article writer correctly identifies the appropriate way to eliminate confusion without resorting to persuading the whole world to adopt this convention. Recast the sentence as “We invited Jan and Ted, as well as our grouchy neighbors” (If Jan and Ted are *not* the grouchy neighbors). Presumably, “We invited Jan and Ted (our grouchy neighbors)” would be the appropriate sentence in the other case.

So, enjoy the Oxford comma if you wish. But that comma will need a lot more devotees before it really starts to add clarity. Even then, it won’t add much.