The first version, T1, did the secure enclave thing, and controlled Touch ID, thermal and power management and a few other things.
The second version, the T2, added storage management, an image signal processor, an audio controller, and encryption for the SSD.
The next version will probably do even more things.
It seems to me that the most likely scenario is the T* chip being used for more and more things and the amd64 chip to be used for less and less things until the amd64 chip is more a "hardware acceleration" chip, like GPUs, here to handle specific tasks to be offloaded from the (now ARM) CPU.
The shift from amd64 as the _central_ processing unit to the T* chip does not need to be a clear cut (ditching the intel cpu directly and using the T* chip for everything) but can (and is) being done progressively (the T chips becoming more and more capable).
For App Store apps, Apple can easily add fat binary support for apps with ARM and x86 code in the same package. They control Xcode and can force resubmission of apps for a future version of MacOS.
The thing is, they need to be able to efficiently emulate x86 at current performance levels for regular software while those developers migrate to the new architecture. This might require new ARM instructions or changes to the graphics processors to assist with performance issues.
The end result is that they need to give their hardware and software folk time and allow developers enough time to get their applications ready. I'm guessing 12+ months from when the new tools become available.
Unless they have been working on it for a while, this suggests 2020 models might be capable.
I would also like to speculate that if they add a fabric interconnect to A13/A14 chips, they could have several sockets in each product resulting in massive performance for the high-end pro models with a very flexible power and thermal budget.
Given their affinity for AMD graphics, I wonder if a desktop A-series processor could have a built in Vega GPU like the Intel chips? The i7-8809G has a Vega with 24 compute units which should be decent for light video or photo work. Notebook Check doesn't have much by way of directly comparable info for the Vega M GH and the A12X Bionic's GPU.
https://www.notebookcheck.net/Vega-M-GH-vs-A12X-Bionic-GPU_8...
https://ark.intel.com/products/130409/Intel-Core-i7-8809G-Pr...
https://reddit.com/r/apple/comments/9w7hzq/it_seems_like_for...