Oxford comma with nonessential phrases

Yes. You are applying two distinct comma guidelines consistently:

• The commas around a nonessential element. (Purdue OWL has some examples.)

• Commas (including the serial comma) separating items in a list of three or more elements. (Number 5 in this list.)

There is no standard guideline for what to do if the application of multiple rules leads to a clusterfudge of commas. Whether you would rephrase or omit the serial comma in your example is an editorial decision. I'd suggest rephrasing if I have a stylistic concern. However, the New Yorker wouldn't; in an article entitled "In Defense of 'Nutty Commas,'" they justify both the use of the serial comma and a low hurdle for considering something a nonessential element. So they have:

“I invited my boss, her nephew, and my acupuncturist to the party.” (straightforward serial comma example)

“Before Atwater died, of brain cancer, in 1991, he expressed regret …” ("of brain cancer, in 1991" is treated as a pair of nonessential elements)

Whatever you choose, be consistent.

This isn't a situation that there are any prescribed rules for to my knowledge. You'll have to make a decision and apply it consistently. My opinion on the matter is that you should ignore the commas around non-essential phrases rule in this case. In my opinion

stifling curiosity, creativity, and ultimately, progress.

is superior to the two forms in your question. Because the stifling of progress is implied to be a result of the stifling of curiosity and creativity, I think it would also be appropriate to say:

stifling curiosity and creativity, and, ultimately, progress.