The situation has gotten more complex since that discussion, too. Modern versions of macOS use an immutable root partition [1]; shipping GPLv3 code in that partition could arguably be a violation of the license.

[1]: https://support.apple.com/guide/security/signed-system-volum...

In addition, there is a clause added (IIRC because of the patent shield licensing deal between Novell and Microsoft) that third party patent licensing needs to cover downstream GPLv3 usage. You cannot simply license a patent for your binary distribution.

So it is possible Apple's lawyers read this section as meaning an injunction against GPLv3 code may be infeasible to solve with licensing the patent, and instead require Apple to make changes on a time-table they would not be happy with.

Sticking to GPLv2 lets Apple control the time table it has taken to license, reimplement or remove components which had moved to GPLv3.

I can't tell you why it took them until El Capitan to remove the Emacs install though.