From the the article you referenced, Chipotle is quoted as saying (emphasis added):
We’ve been working closely with our suppliers to develop new food packaging that is sustainably sourced, functional, compostable, and free of PFAS. We look forward to rolling this new packaging out into our restaurants by the end of the year.
That article is from March 2020, so I looked for anything more recent, and came across this article in Bloomberg Law from June 2021. Here are a few excerpts that mention Chipotle as well as others:
McDonald’s Corp., Wendy’s Co., and Whole Foods Market, Inc., are among at least 15 companies that have announced policies in recent years to phase PFAS out of packaging they use or sell.
Chipotle Mexican Grill, Inc.; Office Depot, LLC; and Koninklijke Ahold Delhaize NV, which owns grocery stores and food delivery services like Food Lion, the Giant Co., and Fresh Direct, are among more than a dozen companies with some type of PFAS in food packaging exclusion policy confirmed by Bloomberg Law.
There are also several regions that are legislating removal of PFAS from food packaging:
Denmark, Maine, New York, Washington, and Vermont already banned PFAS from food packaging, while Minnesota, New York, and Connecticut have purchasing policies barring packaging with the chemicals. California, Minnesota, and Maryland are considering phase-out laws and/or developing regulations.
Bloomberg Law also maintains a PFAS State Activity Tracker, though this hasn't been updated since February 2021.
Finally, the article mentions that some regions are actually testing the products to independently verify if restaurants are following through on promises or complying with regulations:
In Denmark, which banned PFAS in paper and board food packaging in July 2020, none of McDonald’s french fry bags tested contained PFAS. But the french fry bags that McDonald’s sold in the Czech Republic and the United Kingdom did, according to the report.
While it's hard to say if "most" restaurants use disposable food packaging with PFAS, many well-known brands are actively seeking to stop using packaging with PFAS, and state and national governments have implemented or are pursing bans on PFAS. Given the attention that this issue has received, you may be able to find out if a specific restaurant chain uses packaging with PFAS by checking their website or contacting them.