You do need to purchase the font to use it to make the logo.
Forcing an open source project to pay roughly $200 for a one time use is a bad decision. Using such a typeface in a logo is a poor choice because that mean you can't embed it easily for free on the product's website (let's say to use as the font of your titles or to use text on the logo instead of using an image). The problem with embedding a font on a website is that by doing so you are not "using" the font but "redistributing" it.
In the end they used Arvo which was a really good choice, they were able to easily use it all over https://pugjs.org
Typefaces are exempt from copyright in most countries AFAIK. Only the actual font file ("computer program") and name (trademark) are restricted.