All of macOS, since 10.0, is built on ever-more-interlocking systems of ‘intimate’ communication. As upthread points out, there’s a hardware chip that uses IPC to interlock with SIP to protect system files. The depth of IPC used to deliver a Macintosh appears to qualify the entire shipping OS for the “larger program” clause.

Setting IPC aside, it’s still easy to construct a case against GPLv3: If bash is included in an operating system release that can be downloaded like any other program on the Mac App Store, then it’s absolutely plausible to a layperson that the inclusion of GPLv3 in that program would - like any other program - infect it in its entirety with GPLv3’s copyleft requirements. macOS isn’t an aggregate software repository to its users, and a judge could easily be convinced to agree.

I’m not Apple’s lawyer, but I hope this helps convey what I imagine is part of their reasoning against it.