Could an F-35 really be 3% rare-earth?
The ~416 kg is confirmed by multiple sources. The most useful I found[1] uses a comparison:





Product
REE




Mobile phone
0.0005 kg


Air conditioner
0.12 kg


Toyota Prius
15 kg


Lockheed-Martin F-35
416 kg


Navy surface ships
1818 kg


Navy submarines
3636 kg




Based on @MichaelSeifert's input, I've found confirmation for the REE in a Toyota Prius – its curb weight is 1380 kg (toyota.ca):

Each electric Prius motor requires 1 kilogram (2.2 lb) of neodymium, and each battery uses 10 to 15 kg (22-33 lb) of lanthanum. That number will nearly double under Toyota's plans to boost the car's fuel economy. (reuters.com; emphasis mine)

If a Toyota Prius is 1.1–2.3% rare earth by mass, then 3% for the F-35 shouldn't be surprising.
Worth noting:

Despite their name, rare-earth elements are relatively plentiful in Earth's crust, with cerium being the 25th most abundant element at 68 parts per million, more abundant than copper. [emphasis mine]


1: Ganguli, Rajive, and Douglas R. Cook. &quot;Rare earths: A review of the landscape.&quot; MRS Energy &amp; Sustainability 5 (2018). (PDF)