Will earlier Mac Pros be supported in 10.12 at a later date?

I wouldn't count on it. I can't recall a point in the past where older machines were added in during a beta phase. Usually when Apple makes a defining line they stick with it. There may be issues with certain chips in older systems that don't play nice with the new core components in the OS and they decide that development time isn't worth it, or they destabilize the code trying so they just cut it out. I'm sure there is a certain business level decision around it too with it becoming an incentive to upgrade.

Even though the official installer will refuse to install on an unsupported machine, it is often possible to install a new OS on a supported machine and then transfer the drive to the older computer.

This is how I got Yosemite running on a MacPro 1,1 (2006 - yes it also needs

boot.efi

However, a MacPro 4,1 (Early 2009) is running a copy of Sierra I installed on an external drive using a rMBP.

I'd be hesitant to try that..assuming that Apple has chosen to leave older Macs behind for a reason other than to entice the user to buy new hardware... I wouldn't want to risk bricking the machine....or getting such poor performance that putting the new OS on it makes using the Mac unbearable.

Indeed - As well, consider support's reaction when the user pings them for assistance and finds out they're running macfrankenOS

I'll take that chance on support:

I have 20 of these machines to support. NSF doesn't give me money to buy a new cluster every year, never mind that Apple no longer sells server class machines.

You must be a contractor. Be sure the NSF is aware of unauthorized equipment configurations.

I suspect that many people who still actively use a Mac Pro that is older than 2010, have made considerable upgrades to its disk, memory and graphics. As an example, for my early 2009 Mac Pro, I have 16 GB RAM, a 1 TB solid state system drive, 2 4 TB disks and 2 2 TB disks, with an ATI Radeon HD 5770 1024 MB that runs OS X 10.11.15 very well.

I suggest that macOS Sierra for Mac Pros, simply require an adequate graphics card and minimum amount of RAM. From a support standpoint, there is little difference between various Intel-based Mac Pro models; they all have completely 64-bit architectures.

Almost sounds like my machine. I'm running an Early 2009 with 32GB of RAM, 4 HDD (smallest is a 2TB, biggest is a 4TB) and an AMD Radeon HD 6870 (1024MB of GDDR5). I'm rather disappointed that 10.12 won't install on it. As you said, the architectures are almost identical...biggest differences are slightly faster busses and processors (and several smaller variances)

Has anyone tried taking one of their Mac Pro's HD and attaching it a supported mac and then installed on the drive? After the install, put the HD back in the Mac Pro and see what happens. Or an easier method might be to boot the Mac Pro in target disc mode and hook up an supported mac and do the install.