In other words it's not about the overhead, it's about the reliance on x86.
It seems kind of silly to block x86 modes on x64 chips when the backwards compatibility needs of Windows pretty much insures "eternal" x86 modes. It's going to be a while before x86 modes disappear on Intel or AMD chips, and there's evidence to support that like the Itanium (IA-64) failure, and the fact that Windows on ARM made it a commitment to emulate x86 (but not x64) on ARM. x86 is likely going to be a lasting "lingua franca" ISA. Right now I'd almost put more money on x64 being retired before x86, and if anything from that perspective Apple is more tightly coupled to an ISA than before this choice.
That really depends on what their long-term goal is. If the speculation & rumors about an eventual ARM transition have any merit at all, then sunsetting 32-bit support now can help them smooth that transition, since they'll have a lot less work to do to implement whatever Rosetta-esque dynamic binary translator they would need.
Which it seems unlikely that Apple could do in secrecy what Microsoft + Qualcomm could not do (very publicly), but I guess all things are possible.