Before El Capitan, all OS installed fonts where available in all apps. Then Apple started hiding them. As etresoft noted, it's because Apple has always considered them only necessary for document support. What support is that? Good question. In the many previous years of OS X / macOS, I used to whittle the number of active fonts down to the bare minimum the OS needed to work as expected. I never opened a single document that didn't display as intended.
Side note, Athelas is not an Apple font (most of the fonts installed by the OS weren't created by Apple). Athelas is a font created in 2008 by TypeTogether.
Since at least Catalina, Apple has been hiding these support fonts from itself in every app Apple created. Font Book, Pages, Final Cut Pro, etc. In Ventura, the attempt was to hide these fonts from all apps. On my end, even though it hasn't had an update in a couple of years, Ultra Character Map instantly reacted to this change and shows no more of the system installed fonts than Font Book or Pages does.
It seems the Affinity apps are doing the same. Meaning, it's not a mistake, but an intended result. As one example, the Adobe apps completely ignore this change and list all active fonts. At least for now they do.
Why hide them at all? Who knows. And really, what's the difference if you use them? It's just another font. But you're correct that if you purchase Athelas, it will conflict with the installed version and you still won't be able to use it. You'd have to use a font editor to change the internal names to prevent the conflict. But then you'd likely be violating the copyright. And that may not be enough to get around Apple's block.
And going back to another of etresoft's comment, you can open any older document where you used Athelas and the font should appear. You can then possibly copy/paste any line of text from the old document into a new Publisher document to bridge Athelas over to it.
Otherwise, the best solution is to simply use something else. Fonts similar to Athelas. Then you have control of the font at all times. It will no longer matter what Apple does with its installed fonts.